The main characters include:
Major John Sheppard, pilot, 2nd military commander of Atlantis – Joe Flanigan
Dr. Elizabeth Weir, diplomat, head of Atlantis mission – Torri Higginson
Lieutenant Aiden Ford, Sheppard's second-in-command – Rainbow Sun Francks
Dr. Rodney McKay, astrophysicist & serial whinger – David Hewlett
Dr. Carson Beckett, physician – Paul McGillion
Teyla Emmagan, leader of the Athosians – Rachel Luttrell
Dr. Zelenka, physicist – David Nykl

+++ Season 1 (2004/05) +++

01. Rising (part 1)
Dr. Daniel Jackson of SG1 works out where the Ancients have gone and Dr. Weir leads an expedition on a one-way trip to the city of Atlantis on a planet in the Pegasus galaxy. Gen. O'Neill is nearly wiped out by a rogue Ancient weapon before they leave! The expedition emerges through a stargate in an underwater complex which powers up automatically. Then they find that the power system is failing and the place is being flooded. A team goes though the stargate in search of another world as a refuge. They arrive on the homeworld of the Athosians as the Wraith arrive to harass the inhabitants of the other world; as they have been doing regularly for generations.

02. Rising (part 2)
Dr. Weir orders an evacuation as the power supply in the city is failing. She is about to head for the planet attacked by the Wraith when the shield fails and the city suddenly rose out of the sea! Hotshot pilot Sheppard takes an Ancients' ship through the stargate to the gate in orbit around the Wraith world on a rescue mission. Col. Sumner has the life drained out of him by a bright-red-haired Wraith whom Sheppard kills. But she is just a caretaker and the rest of the Wraith wake up; which puts the galaxy in great peril. After a space battle, Sheppard gets the rest of the prisoners back to Atlantis.

03. Hide & Seek
McKay takes some gene therapy then he puts on an Ancients' shield; and find he can't get it off, which means that he can't eat or drink until it is finally switched off. One of the Athosian kids finds a transporter device and lets an entity out of a storage module. The Ancients had been studying the being and it eats energy. So the Earthers lure it to the stargate and McKay activates his device again so that he can stroll into the creature's black fog and make it chase a naquadah generator through the gate to a desolate world.

04. Thirty-Eight Minutes
Jumper One gets itself stuck half in and half out of the stargate, and stargates can't stay open for more than 38 minutes, so that is how long the Earthers have to crack the problem. Worse, Sheppard has an alien creature stuck to his neck and a Wraith took one look at him and gave him up for dead. The doctor suggests using a defibrilator to stop Sheppard's heart; which makes the creature release him. Then they have to blow a hatch to vent atmosphere and move Jumper One through the gate when the obstruction has been cleared - and the creature is spaced in the process.

05. Suspicion
The Wraith keep arriving on new worlds visited by the Earthers. Security Sgt. Bates suspects the Athosians. When McKay manages to open the roof on the jumper bay, and Sheppard finds land on an exploration flight, the Athosians end up relocated; all but Teyla. McKay discovers that a necklace given to her by her father has a gadget for detecting Ancients, whose genes live on in humans. So Sheppard uses the necklace to take one of the Wraith prisoner.

06. Childhood's End
A jumper crashes on a new planet full of kids with bows & arrows. They think killing themselves on the day before they turned 25 will has kept the Wraith away for 500 years. McKay finds they have a shield, which stops electronic equipment from working and he nicks the Zero-Point Module from it. So a Wraith beacon started transmitting again! Sheppard tries to talk the leader of the group out of suicide while having to cope with his nutty successor. And McKay has a hell of a struggle to get the beacon working again when he finds that the ZPM be no of use at Atlantis.

07. Poisoning The Well
The Hoffans have been working for 150 years to perfect a drug which will interfere with the Wraith process for drawing life-energy from humans. The Scottish doctor helps to develop the drug but he and Dr. Weir are not happy about letting a dying Hoffan test it using the Wraith prisoner. The unhappiness level multiplies when both the volunteer and the Wraith croak. By then, the Hoffans are treating the whole population even though the drug is killing 50% of the people treated. The Earthers point out that the Wraith will exterminate them, rather than harvesting them, if they can kill feeding Wraiths. But 96% of the Hoffans vote to go ahead anyway. So the Earthers leave, expecting the Hoffans to be wiped out totally after the next Wraith attack.

08. Underground
The Earthers try to trade for food with the Genii - apparently simple farmers led by Commander Cowen (Chief Meany from Startrek TNG and Deep Space 9). But McKay and Sheppard find a bunker where the Genii are trying to make an atom bomb. So McKay tells them he made one for his school science fair. The Genii have a piece of Wraith technology which gives the locations of hibernation ships, which they plan to nuke. The Genii turn nasty after a recon mission, so Sheppard trump their ambush with a couple of Jumpers and strolls off with the Wraith gadget. And when its data is decrypted, the Earthers find that they are up against at least 60 Wraith hive ships; far too many to take out all at once.

09. Home
The Stargate Atlantis crew find a planet with a gate which draws power from the foggy atmosphere; enough to open a wormhole to Earth for a one-way trip. But when Dr. Weir, McKay, Sheppard and Teyla get to Earth, they soon find things don't add up. ‘General Hammond' admitted being an energy-based inhabitant of the foggy planet. ‘He' says using the stargate for a trip to Earth would kill millions of his people and they created an illusion for the Earthers to enjoy until their bodies starve to death on ‘his' planet. But the Earthers manage to talk him into letting them return to Atlantis.

10. The Storm (part 2)
A megastorm is brewing and with no force field, Atlantis looks doomed. The Mnarians offered to shelter everyone for a couple of days but they sell out the Earthers to the Genii. McKay comes up with a plan to use the lighting from the storm to power the force field temporarily. Tayla and some others are stuck on the mainland when Kolya and a thieving gang of Genii takes over Atlantis. Everyone but Sheppard is captured, the plan to power the force field goes up in smoke when the Genii shoot up a control panel. And at the end, Kolya threatens to shoot Dr. Weir.

11. The Eye – The Storm (part 2)
Atlantis is still being battered by the storm. McKay persuades Kolya not to kill Dr. Weir. Sheppard takes out more of the Genii assault force while McKay & Weir are repairing the switching gear to disconnect the last grounding station. The eye of the storm passes over the jumper on the mainland, which allowed it to return to the city. Teyla got into a punch up with one of the female Genii. Sheppard gets control of the shield on the stargate and 50+ Genii reinforcements are killed when they try to reach Atlantis. The survivors gate out and McKay's plan works; the energy from lightning hitting the city powers up the force field as a tsunami hits it. Sora of the Genii remains on Atlantis as a prisoner.

12. The Defiant One
Sheppard & Co. investigate a crashed Wraith ship and find one still alive. It eats one of the crew and munches another. Working from intuition, Dr. Weir sent off a rescue mission, which will take 15 hours to arrive. The Wraith takes over the jumper and gets into a shooting war with Sheppard. The man who was ‘fed from' and aged shoots himself to get away from McKay's whining. And the rescue mission arrives just in time to splat the Wraith as it is eating the local glow-bugs.

13. Hot Zone
Two of the crew die while McKay and a team are checking the city for structural damage after the storm. McKay thinks it might be the plague that killed the Ancients. Dr. Weir wants everyone to stay where they are. McKay finds some storm-smashed virus containers in a laboratory. Another woman goes wild and croaks. Sheppard pulls rank on one of his men to get himself released from a gym despite Dr. Weir's objections.
   One of McKay's party forces his way to the mess hall, contaminates everyone there and the main computer locks down the city. McKay deduces that a nanovirus built to kill humans has been released and he tells Sheppard to trigger an electromagnetic pulse to kill the virus. The first try doesn't work but Sheppard overloads a naquita generator in the atmosphere. McKay and the doctor conclude that neither the Ancients nor the Wraith created the virus. And Dr. Weir isn't happy about Sheppard over-ruling her when he thinks the military situation warrants it.

14. Sanctuary
An energy weapon zaps Wraith ships as they are about to destroy a jumper full of Stargate Atlantis personnel. Sheppard & Co. land on a planet called Proculus hoping to find a Zero Point Module. Instead, they find a pre-technology culture with a deity called Athara and a priestess called Chaiya. The Wraith have never attacked Proculus but Athara refuses to offer sanctuary to refugees from other worlds. Sheppard takes Chaiya to Atlantis. McKay is sceptical about the whole religion thing, he scans Chaiya and finds her totally disease-free and too perfect; and he is proved right.
   Chaiya, who fancies Sheppard, is Ascended but she broke their code of non-interference by defending her world against the Wraith. The other Ascended will stop her doing so if out-siders take refuge on Proculus. As Chaiya is the source of the 'energy weapon', there is nothing on Proculus for the Atlantis crew but Sheppard offers to visit the lonely Chaiya.

15. Before I Sleep
On Dr. Weir's birthday, Sheppard finds a 10,000 year old woman in a stasis chamber. She knows the team at Atlantis and she claims to be a Dr. Weir who has been time-travelling. DNA testing confirms her story. In her time-line, the city didn't switch on when her team arrived and more or less everyone drowned when the city locked down and the shield collapsed. Weir, Sheppard and a boffin escaped in a ship with a time-travel gadget. Only Weir survived the trip back in time.
   The council of Atlantis ordered the time machine to be destroyed so Johnas, the inventor, beefed up the city, including installing the fail-safe which took the city to the surface, but someone had to stay behind to rotate 3 ZPMs to give it power. The people of Atlantis headed back to Earth and Weir stayed behind in the stasis chamber. She was supposed to be revived when the team from Earth arrived, but McKay shut off what he thought was an unexplained power drain. Before she croaks, Weir handed over the co-ordinates of 5 outposts, all known to have a ZPM. And at the end, Dr. Weir scatters her other self's ashes over the city.

16. The Brotherhood
A team from Atlantis visits the planet Dagan in search of a zero-point module to restore the city's shield and protect it from the Wraith. The Ancients gave a ZMP to ‘The Brotherhood' but the Wraith wiped them out. Kolya and a Genii team watch McKay and Allina, a local archaeologist locate 8 of 9 marker tablets and then an underground bunker, in which the Genii trap the Earthers. At Atlantis, Dr. Zelenka finds out that the city has deep-space sensors, which is handy as a Wraith dart is approaching. It scans the city, destroying a jumper in the process, then self-destructs after transmitting data into deep space.
   McKay and Allina find the last tablet. A Genii is killed by the device on which the tablets have to be mounted. Sheppard, who's bright enough to be in Mensa, works out how to operate it. Then Lt. Ford lets off a stun grenade and the Genii are overpowered. But everything goes wrong when the Earthers think they have their ZPM. Allina is the leader of The New Brotherhood, she knows from what McKay told her that the Earthers are not Ancients and she intends to hide the ZPM away and worship it until the Ancients return. So Sheppard & Co. return to Atlantis empty handed – to learn that 3 Wraith hive ships are just 3 weeks away.

17. Letter From Pegasus
Dr. McKay thinks the Atlantis team should send a message back to Earth with the Wraith approaching. He can power up the stargate for 1.3 seconds and send an ultra-compressed data burst containing a warning about the Wraith, all the station's logs and brief personal messages.
   Dr. Zelenka spots that the Wraith hive ships are dropping out of hyperspace to harvest humans. Sheppard and Teyla take a jumper to the next destination via the stargate to gather data.
   As the Atlantis team compose their messages, Sheppard and Teyla watch the Wraith sweeping up everyone they can find. Teyla wants to rescue some of the people and the jumper returns to Atlantis packed with refugees. And the message gets through to the SGC.

18. The Gift
Teyla is having nightmares about the Wraith and Dr. Zalenka warns that the hive ships are a week away. Major Sheppard wants to fight and the scientists think he'd nuts. When he stands Tayla down, she agrees to talk to the station psychiatrist. She can sense the approach of the Wraith and there are a few like her in every generation. An old Athosian lady tells her a few people were taken from a planet and returned, and they passed on the Gift.
   Teyla has the gate address of the planet and she thinks the Gift might be a way to fight the Wraith. There is an abandoned Wraith lab on the dead planet. Dr. Weir thinks the Wraith evolved after the Ancients arrived; a cross between insects and humans who became their food; as tThe Wraith language is derived from Ancient. Teyla has Wraith DNA and the next conclusion was that a Wraith scientist was experimenting on humans to make the feeding process better. And as a result, Teyla can hear Wraith telepathic communications.
   Under hypnosis, Teyla visits a Wraith ship but a Wraith takes control of her until she is shocked back to normal consciousness. Then the Wraith attack the Alpha Site, leaving the people at Atlantis with nowhere to go. Teyla thinks there are more Wraith awake than the food supply can sustain. One of the crew has to shoot her with a paralyzer gun when she gets violent after being hypnotized again; but she can tell Weir that the Wraith want to take Atlantis to get to a new, rich feeding ground; Earth!

19. The Siege (part 1)
Dr. McKay thinks an Ancients' defence satellite could be powered up with a naquitah generator. Dr. Zalenka is worried about being able to destroy the city and the Ancients' database. Major Sheppard isn't having much luck finding an alternative Alpha Site. Security Sgt. Bates accuses Teyla of being controlled by the Wraith and she decks him. The Athosians don't want Weir to blow up the city as it is sacred to them. Bates is found bashed; Teyla says it wasn't her. Dr. Weir asks Zalenka to back up the database but he can manage no more than 9% of it.
   McKay gets to do an EVA to repair the satellite. Bates was attacked by a Wraith, the pilot of the ship which buzzed the city in episode 16. Dr. Zalenka comes up with a Wraith detector. One of the crew is left aboard the satellite, which takes out one Wraith hive ship before it is destroyed. Teyla helps to capture the Wraith and Sheppard shoots it full of holes while trying to interrogate it. And finally, Dr. Weir orders the evacuation of Atlantis.

20. The Siege (part 2)
As the Wraith hive ships close in, Dr. Weir activates the self-destruct to destroy Atlantis. But a team from Earth arrives to relieve her team. The message in Episode 17 got through, a Zero Point Module was found in Egypt and the Marines are there to defend the city for the 4 days which a ship will take to bring the ZPM to the Pegasus Galaxy to power the city's shields. Colonel Everett tries, and fails, to sideline Weir and Teyla. The Marines have brought space mines and a power source for the Ancients' chair. The Wraith take out the mines with asteroids and blind the sensors with the radiation released.
   There is lots of shooting when Wraith darts attack Atlantis. Teyla warns that Wraith are in the city; they beamed down just before their darts crashed. Col. Everett has to let the Athosians help with hunting them. Major Sheppard asks the Genii for a couple of nukes to put in jumpers remotely controlled from the chair. The Genii have some fun and games with Dr. Weir but they eventually co-operate in return for some C4.
   The bad news is that the nukes need a day's work to make them work. The worse news is that the Wraith have sabotaged the power system and the jumpers can't be controlled from the chair. Col. Everett is eaten by a Wraith (apparently). Sheppard volunteers himself to fly one of the jumpers in stealth mode. He closes in on the Wraith hive ships as the self-destruct is activated again. To be continued . . .

+++ Season 2 (2005/06) +++

   The characters further include:
Colonel Steven Caldwell, captain of the Daedalus – Mitch Pileggi, and
Ronon Dex, former Wraith prey – Jason Momoa; plus, of course,
The Wraith

21. The Siege (part 3)
As the Wraith attack Atlantis, the Earth ship Daedalus arrives with Asgard technology and a ZPM to power the shield. So Sheppard is saved, Teyla saves McKay from the Wraith as he is taking the ZPM to the shield generator, and the last hive ship is taken out with the Asgard weapon. The surviving Wraith dive their ships at Atlantis but McKay gets the shield working just in time to make them splat harmlessly.
   Lt. Ford is recovered from the sea along with a dead Wraith, which was feeding on him (while injecting an enzyme) when they were blown up. The enzyme kept him alive but Ford is now dependent on it and a sort of super-strong vampire with very little self control. Dr. McKay finds that 12 more hive ships are 36 hours away and heading for Atlantis. Sheppard suggests an ambush one hyperdrive jump from the city.
   Daedalus kills 2 hive ships before it is forced to head back to Atlantis, damaged. The Wraith bombard the shield so Sheppard suggests cloaking the city and faking a self-destruct explosion to make the Wraith believe the Earthers are no longer a threat. Teyla sends a message to the Wraith telling them about the coming big bang. So the Wraith stop shooting.
   A nuclear blast blinds the Wraith sensors and they accept that the city has been destroyed and leave the area. Meanwhile, Ford picks that moment to fire up the stargate and decamp in a jumper with the supply of Wraith enzyme, which Dr. Beckett harvested from the bodies.

22. The Intruder
Daedalus is on the way back to Atlantis from Earth and the episode is intercut with washed-out flash-backs to events at the SGC. General Landry wanted a new military commander, Colonel Caldwell, CO of Daedalus wanted the gig but Major Sheppard was promoted to lt. colonel.
   A Dr. Monroe is killed and McKay tells Col. Caldwell it wasn't an accident. Another crew member is trapped in an airlock and spaced. The Asgard aboard finds a self-modifying virus in the ship's systems and it's Wraith. It lay dormant near Earth but it became active when the ship got close to Wraith space and it's killing the people who could expose it.
   The virus starts sending out a distress signal to summon the Wraith so Sheppard shoots up the transmitter array and then finds himself speeding away from Daedalus with the virus in charge of his fighter! So he does a flashback to meeing Lt. Ford's cousin while waiting to be beamed back to Daedalus. McKay reboots the ship and during the blackout, Dr. Weir remembers her husband(?)boyfriend not wanting to go to Atlantis as he's found someone else.
   The virus returns, sending the ship close to a star to kill the crew. McKay tries to give the virus no hiding place but the second reboot doesn't work because the virus is lurking in the fighter from which Sheppard was beamed. So Sheppard has to take it out flying another fighter manually. And a third reboot works.

23. Runner
Two explorers from Atlantis find a dead Wraith and Dr. Beckett deduces that Lt. Ford killed it. Sheppard leads a team to the planet, which has a very bright sun. Colonel Caldwell wants Sheppard to kill Ford if he's a threat. Teyla and Sheppard are captured by Ronon, a dreadlocked Runner into whom the Wraith have planted a tracking device. They have been chasing him for 7 years and killing anyone who gives him shelter.
   Ford captures Dr. McKay and tells him he feels 'better than fine' and he doesn't want the doctor on Atlantis messing about with him. Teyla and Sheppard get free briefly. Ronon tells them that if they get the tracker out of him, he'll help them find Ford. Dr. Beckett gets the job and he has to cut the tracker out while Ronon holds a gun on Teyla (and Sheppard keeps the Runner in his sights from a distance).
   McKay shoots Ford; with little effect; 3 Wraith darts come through the planet's stargate, and McKay ends up hanging from one foot in a trap. The Runner does battle with Ford as he's about to shoot McKay. Sheppard has a confrontation with Ford, who deliberately runs into a Wraith beam and gets himself removed from the planet. And back on Atlantis, Ronon finds that his planet has been harvested and destroyed by the Wraith.

24. Duet
McKay and Lt. Cadman are taken by a Wraith dart, which is shot down. Dr. Zalenka says he can see 2 life forms in the dematerializer but there's only enough power to extract one of them. McKay is retrieved, the wreckage is taken to Atlantis and McKay finds he can hear the female Lt. Cadman in his head. She offers to tell McKay about women as he's making a mess of acquiring a love life.
   Sheppard wants to recruit Ronon, who upsets him by training with Teyla. McKay wakes up in Cadman's bed and finds that she can take over his body when he 'lets go'. McKay collapses and Dr. Beckett says one of them has to let go or they'll both die. Dr. Zalenka's experiments with mice and the dematerializer aren't working out.
   McKay suddenly realizes that he can solve the problem by adding a crystal from the stargate to the dematerializer. He is then zapped with the dematerializer and restored as both himself and Lt. Cadman. And at the end, Dr. Weir gives her okay to Ronon joining Col. Sheppard's team.

25. Condemned
Col. Sheppard & Co. run into stroppy natives and they have to fight their way back to their jumper with the help of the local authorities on Elysia. The Magistrate tells them the stargate is on a prison island because the Wraith are content to harvest the condemned prisoners and not attack the rest of the planet, which is almost crime free. He also says the planet has a mineral which gives a non-radioactive, fissionable material, which could be the basis of trade.
   Flying back to the stargate, the jumper is shot down and crashes on the island. Terel, the leader of the prisoners, does an accurate character assessment on McKay and threatens to kill Sheppard, Teyla and Ronon one at a time to force McKay to fix the jumper. Meanwhile, Dr. Weir arrives with a rescue mission in stealth mode. The Magistrate promises to find the missing crew.
   McKay thinks he can dial the gate from the jumper, everyone escapes from the prison hut but Terel was listening in on a concealed radio. A Wraith ship arrives to visit the Magistrate, with whom the commander is on drinking & eating terms. The Wraith want more humans to feed on, which means more prisoners have to be sent to the island for minor crimes. When Dr. Weir finds out what's going on, she breaks off relations with the Elysians.
   Sheppard & Co. are captured just after McKay fixes the dialler and the opportunity to use it is lost. A Wraith cruiser arrives but Sheppard damages it with the jumper's weapons. Weir's jumper dials another planet and the prisoners escape from the island. Then the humans return to Atlantis and the Wraith harvest the rest of Elysia.

26. Trinity
Sheppard & Co. find the wreckage of a Wraith fleet orbiting a dead planet, on which there is an intact Ancients' outpost, where there is a weapon similar to the one used to take out Wraith hive ships at Atlantis [see Episode 19. The Siege (part 1)].
   Meanwhile, Ronon goes on a trading mission with Teyla to get away from Atlantis, and screws things up. But there's another survivor from his planet, Solan, in the village. Solan turns out to be from Ronon's regiment and there are 300 other survivors still around, including Kell, Ronon's task master.
   McKay thinks the weapon uses the ultimate power source; vacuum energy; which will make ZPMs obsolete. He thinks the outpost is the Ancients' Manhattan Project. McKay and Zalenka think they can finish the Ancients' work. McKay's test kills a member of the team, he wants to carry on but Dr. Weir won't let him. So McKay asks Sheppard for his backing, insisting the Military will want vacuum energy.
   McKay thinks the Ancient's calculations were wrong and he's right. Dr. Weir, against her better judgement, gives him another chance but not at full power. Dr. Zalenka thinks the power source can't be controlled at any power level as it creates exotic particles which can't be controlled in our space/time. Zalenka also thinks the weapon killed everyone at the outpost, not the Wraith, but McKay doesn't want to hear this.
   Ronon shoots Kell as soon as they meet because he was a traitor and a coward who sacrificed others when he fled from the Wraith; and Teyla is inclined to agree with him. McKay loses control of the weapon again and it starts shooting. So Sheppard has to do some fancy flying to get to orbit and Colonel Caldwell in Daedalus saves the team's collective asses. And McKay has to go round apologizing to everyone at the end.

27. Instinct
Sheppard & Co. visit a planet where people aren't going out at night because of the Damus, which is due to start feeding. A Wraith ship crashed on the planet 10 years ago, the locals killed the survivors but one got away. Teyla senses something different about the Wraith when the team goes hunting. Ronon tracks it to a cave, where they find Zadek, who says Ellia is his adopted daughter. He had just lost his family when the Wraith ship crashed and he adopted a child survivor.
   There was another Wraith in the forest but Zadek claimed to have developed a brew which let Ellia survive on normal food without 'feeding' on humans. Dr. Beckett thinks young Wraith eat normal food then something changes in them which makes their digestive system useless. He is developing a retrovirus from the DNA of the eratos bug which attacked Sheppard in Episode 4, Thirty-Eight Minutes. He hopes it will eliminate the bad DNA in a Wraith and leave just the human part.
   Dr. Beckett goes to the planet. Sheppard & Co. hunt the male Wraith, which is now going out in daylight; and so do the villagers. After listening in on Dr. Becket talking to Zadek, Ellia injects herself with the retrovirus. She doesn't want to be different and she tells Zadek his serum never worked. The retrovirus has the opposite effect of destroying Ellia's human DNA.
   Ellia kills the other Wraith and Zadek is fatally injured. His father arrives with the villagers and we learn that Zadek is only 34 even though he looks as old as his dad. He let Ellia feed off him while developing his serum, then she joined the other Wraith on hunts. So she has to be killed, too.

28. Conversion
The injury on Sheppard's arm, inflicted by Ellia, heals before Dr. Beckett's eyes. Sheppard finds that he can run Ronon into the ground and beat Teyla at double-sticks; and get inappropriate with her. He has been infected with the retrovirus and Beckett can't predict what will happen. Eratos bug stem cells are the answer, Beckett decides, so a team goes out to collect some bug eggs.
   Col. Caldwell takes over from Sheppard as head of the military as Sheppard is changing into a bug and he isn't safe to be around any more. Caldwell upsets Dr. Weir by trying to make lots of changes. The egg-collecting expedition loses two men. Sheppard tells Dr. Weir to kill him or try again. The doctor puts him into a coma and he has 24 hours left.
   Dr. Beckett eventually realizes that Sheppard has changed so much that the bugs will think he's one of them. So he goes into the cave and retrieves a supply of eggs. And 2 weeks later, he's 100% John Sheppard; apart from a small remainder patch of bug cells on his right forearm.

29. Aurora
With the new ZPM, Atlantis' systems are at full power, a beacon has been activated and Ancients' spaceships are returning to the city. Daedalus goes to meet Aurora and destroys a Wraith dart. The crew are still aboard the wreck of Aurora. They have been in stasis pods for 10,000 years. Dr. McKay finds out that they are in contact mentally in a virtual reality environment. McKay decides to get into a spare pod and questions the Ancients for information, which will help in the current war with the Wraith.
   Sheppard gets into the pod because he is more expendable than McKay. The crew of Aurora are trying to soup up their hyperdrive and they don't seem to know their ship is a wreck. The captain knows of a weakness in Wraith technology but he puts Sheppard in the brig instead of sharing it. 2 Wraith cruisers come looking for the dart so Col. Caldwell gives McKay 30 minutes to produce results.
   Teyla and Ronon find a Wraith in a stasis pod and linked to the neural net. Caldwell wants to kill it but McKay wants to find out what the Wraith is doing. McKay realizes the Wraith is playing Aurora's stroppy female first officer, controlling the VR set-up and trying to get hold of the secrets of the Ancients' galactic hyperdrive. McKay switches off the Wraith's pod and gets chased; but Sheppard shoots the Wraith.
   Aurora's captain activates the self-destruct, which takes care of the Wraith cruisers. The information on the weakness was in a file on the computer, which had been erased. The captain knew only of its existence and nothing of the contents. But Sheppard gets the people on Atlantis to drink a toast to Aurora's crew anyway.

30. The Lost Boys (1)
Following a tip on another ZPM, Sheppard & Co. were ambushed, kidnapped and taken through the local stargate to another planet. Lt. Ford was behind it. After being harvested by the Wrait dart [episode 23. Runner], he killed the pilot for its supply of enzyme and built up a gang of followers, all of them on the enzyme. Ford also had a larder of live Wraith to ensure continuity of enzyme supply.
   The prisoners were having a meal when Ford announced that the enzyme had been incorporated into their food – all but Sheppard's. His role was to be a witness and confirm that taking the enzyme was a good thing. McKay found that Ford had removed the crystals from the local stargate, so the team was stuck.
   Ford sent Sheppard and Teyla on a mission to see how his team worked; which turned out to be crash, bang and casualties accepted. Dr. McKay got to hang out with Ford's boffin, who thought that the Wraith were fragmenting and becoming rivals due to the lack of food supply in the galaxy. Ford's big plan was to blow up a Wraith hive ship and he had a Wraith dart, which he wanted Sheppard to fly. McKay thought it was a bad idea but Sheppard thought his team might be able to use the DHD in the dart to escape.
   On Atlantis, Dr. Weir was sending out teams to search for Sheppard & Co. but Dr. Zalenka wasn't optimistic after finding 50 possible gate addresses, with no time signatures, stored in the DHD used by the kidnappers. The military felt that the search could take months, which wasn't acceptable to Dr. Weir.
   Ronon and Teyla got stronger and more aggressive. McKay, off the enzyme, fixed the dart. Then Ford made McKay a hostage to make Sheppard co-operate. The dart went onto autopilot on entering the hive ship, some of Ford's men were lost when Sheppard rematerialized them from the cargo hold. Sheppard had to shoot some Wraith and alarms went off. At the end, the survivors ended up in the cell block and a Wraith strolled off with Sheppard.

31. The Hive (2)
The Wraith queen wanted to know where Sheppard got the dart, which was used to infiltrate her hive ship and Teyla sensed that she was agitated because another hive ship was approaching. At Lt. Ford's base, Dr. McKay was looking for a way to get hold of the crystals for the DHD. He solved the problem by taking a large dose of the enzyme and beating up anyone who got in his way. Sheppard & Co. escaped from their cell and released some prisoners, but they were recaptured.
   McKay reached Atlantis an incoherent wreck and had to go 'cold turkey' in the sickbay. The prisoners of the Wraith were having the same problem and one of Ford's men croaked. Daedalus arrived at Atlantis before McKay returned to what passes as normal for him. McKay thought he could warn the hive ship's target that there was a cull on they way and beam the team from Atlantis off the Wraith ship.
   Sheppard told the Wraith queen that he'd seen through her plan to put an infiltrator among his team and she confirmed that Nira, Sheppard's cellmate, was one of many thousands of Wraith worshippers. So Sheppard told her that he was in league with the queen of the other hive ship. Then Ford arrived shooting. He held the Wraith at bay while Sheppard freed the other prisoners.
   Daedalus found 2 hive ships instead of one, which complicated finding the team from Atlantis. Sheppard attacked one of the hive ships with his stolen dart and got them to shoot each other to bits. Daedalus scanned the wreckage after the big bang but found that no darts had survived. But Sheppard, Teyla & Ronon returned to Atlantis via the stargate, having used the dialer on their dart, to report growing tension and conflict among the Wraith over scarce food resources.

32. Epiphany
Dr. McKay detected an energy spike while a Jumper was flying over mountains and he found a doorway. Everything looked okay when he stuck a camera through the portal on a stick, so Col. Sheppard went through. One small problem – he entered a zone where time was passing at the rate of 12 minutes per 3 seconds to time outside. Sheppard went off to explore before McKay realized what was happening and threw supplies through the portal.
   Sheppard tangled with an invisible beast and met people living inside the time bubble, which was a sanctuary where the people were meditating and trying to Ascend. McKay found a crater in which the time bubble was located. He hoped to land a jumper but an experiment showed that the tidal forces at the border were too severe to penetrate except at the portal.
   The people in the time bubble were pilgrims with unusual powers. A child had the power to heal, and she patched Sheppard up again when he tangled with the beast again. One of the women knew that Sheppard was the key to defeating the beast and helping them to Ascend. Sheppard had a problem with their wish to Ascend to a higher plane of existence when they had done nothing much on this plane apart from meditate.
   McKay took the usual gang through the portal, intending to switch off the power source for the time bubble. The beast attacked and it had become huge. No surprise when it turned out to be the fears of the pilgrims. They believed Sheppard gave them the courage to face those fears, the beast was destroyed. The pilgrims Ascended after warning McKay to leave the power source alone, and the gang from Atlantis was allowed to go home via the portal.

33. Critical Mass
Dr. Zalenka is shipped off to a planet of kids as two Wraith cruisers approach Atlantis. Dr. McKay detects energy bursts which suggest they're shooting at each other. Meanwhile, on Earth, the Goa'uld have infiltrated the Trust and most of Earth's institutions, and they've planted a bomb on Atlantis as a means of stopping the Wraith getting to this galaxy. General Landry is told that the bomb will go off the next time Atlantis's stargate dials Earth to deliver reports; like, in a couple of hours. And there's no way to deliver a warning to Atlantis.
   On Atlantis, Teyla takes Dr. Beckett to see an ancient female friend. She's dying, which is a somewhat unnatural end for the Athosians, given the Wraith situation. On Earth, Dr. Lee suggests using a chain of sub-space transmitters to relay a message to Atlantis, and including Daedalus in the chain. So the spaceship has to travel back toward Atlantis to get in range. The Asgard aboard reckons he can modify the hyperdrive to get into transmission range before the drive burns out.
   The message arrives in the nick of time and Dr. Weir recalls Daedalus to Atlantis to try to locate the Goa'uld agent, who must be aboard the spaceship. The stargate tries to dial Earth but fails as Dr. McKay has taken the ZPM off-line. But a distress beacon goes off and the Wraith cruisers head for Atlantis. Dr. Weir tells Col. Caldwell she'd in charge of the hunt for the agent and starts grilling suspects.
   There's no bomb; the fail-safes have been disabled so that the ZPM will overload when large amounts of power are required, such as when the stargate is dialled or the shield is raised to hide the city from the Wraith. So McKay has to switch off other systems to try to stay below overload level.
   A stroppy Dr. Kavanagh becomes the prime suspect as the agent. Teyla's friend refuses to let Dr. Beckett prolong her life with a pace-maker. The city's inertial dampeners begin to power up and the ZPM heads for an overload. Dr. Weir okays violence but Kavanagh faints before Ronon can get to work on him. Weir starts an evacuation plan as the Athosians hold a ceremony for the dead woman.
   Shock-horror! Col. Caldwell is the infiltrator! And he's a Goa'uld. Ronon works him over a bit then Sheppard uses a taser to stun the Goa'uld and let Caldwell provide the computer access code for the fail-safes just in time.

34. Grace Under Pressure
A repaired jumper crashed into the sea and McKay and the pilot woke up sinking and getting to crush depth for the cabin's windows. The pilot, for no apparent reason, shoved McKay into the rear compartment but didn't join him. Perhaps he preferred death to McKay's whingeing. Dr. Zelenka, who had done the repairs and who had got McKay to replace him on the test flight, was given the job of locating the jumper.
   McKay did a lot of ranting at unco-operative computer systems, then he started hallucinating and conjured up Samantha Carter. Sheppard came up with the idea of turning another jumper's cloak into a shield, which would let it descend below crush depth for 30 minutes. Dr. Zelenka got to go along on the undersea grappling mission to make the modifications to the cloaking system.
   Phantom Sam Carter told McKay to stay alive and not waste power on a plan which was bound to fail. The jumper reached the bottom of the sea and the rear compartment began to take in water. Phantom Sam tried to warm McKay up a bit but he thought she was trying to sabotage his plan; which flopped. Meanwhile, Sheppard & Zelenka detected a sea monster 6-8 times the size of a jumper, which was taking an interest in McKay's jumper.
   McKay's jumper had taken in so much water that the cable on the grapple wouldn't stand the strain of lifting it. Dr. Zelenka came up with the idea of extending the shield to include both jumpers. Sheppard walked across to McKay's jumper and banged on the door, telling him to open up. Which left McKay, who was seeing a Phantom Sam Carter, with the problem of deciding if Sheppard was real or just another hallucination. Phantom Sam told him to trust his friends, and he was saved.

35. The Tower
Sheppard & Co. arrive on a primitive world protected from the Wraith by 'The Tower', which turns out to be a city-spaceship the size of Atlantis buried with just the middle bit showing. Sheppard gets into a confrontation with troops from the Tower and Otho, the chamberlain, gives him a demo of their drone weapon, which is the same as the one in Antarctica on Earth.
   Sheppard is taken to the Tower and finds the interior is terribly Ruritanian. The Lord Protector has the Ancient gene which lets him use the 'throne chair', he collects half of the harvest from the surrounding region and the feasting in the Tower is positively mediaeval. The Lord Protector is a heart attack waiting to happen and there's a battle for the succession. Mara, his daughter throws herself at Sheppard, stark naked, because Otho finds he has the Ancient gene more strongly than anyone in the royal line for 300 years.
   Sheppard brings Dr. Beckett to the planet as McKay ventures into the earthquake-prone catacombs below the Tower. Sheppard tells Otho that gene therapy will create lots of people able to control the chair and Dr. Beckett finds that the Lord Protector is being poisoned. Ronan takes out a squad of guards.
   McKay and his guide are trapped by an earthquake, which blocks their radio. The Lord Protector dies and Otho announces that he is taking over. He takes Sheppard and Dr. Beckett prisoner when he hears that Ronan and Teyla have started an uprising in the village. McKay finds auxiliary control and uses a drone to blast a hole to the surface to restore radio communications.
   Mara takes a radio to Sheppard and tells him Otho plans to destroy the village as an example. McKay powers up the stardrive and to drain power from the ZPM and prevent Otho from using the chair. Otho is killed with his own poisoned dagger. Atlantis and the people on the planet then make a deal to exchange drones and a jumper for medicines and Earth's help and advice.

36. The Long Goodbye
Sheppard found two orbiting 'coffins' with life-signs and Col. Caldwell returned to Atlantis free of his Goa'uld. The 'coffins' turned out to be stasis pods for a single occupant. When the one containing an old woman was opened, Dr. Weir was zapped by a beam of light and she became a temporary host for the woman's consciousness. Phoebus said the man was her husband and they'd been attacked by the Wraith.
   Sheppard became the host to Phelan's consciousness and then the shooting started. The aliens zapped everyone in sight then started hunting each other through the city. McKay tried to take command of Atlantis as next in line behind Weir & Sheppard but Col. Caldwell slapped him down. Phelan knocked out the power supply, bamboozled Ronan into thinking he was talking to Sheppard and got Ronan shot by Phoebus. Dr. Beckett had to perform a life-saving operation by torchlight.
   Phoebus locked down the city, almost decapitating Teyla, who zapped Phelan/Sheppard. Phoebus then ordered Teyla to shoot Phelan or she would kill three-quarters of the people in the city. She and Phelan were left-overs from a long-forgotten war and she was thought killing Phelan meant that her side would win.
   McKay cracked Weir's command code and prevented Phoebus from carrying out her threat. Teyla gave Sheppard a stunner to shoot Weir after his 'possession' seemed to wear off; but Teyla still didn't trust Sheppard. Both Weir and Sheppard ended up in sickbay, unpossessed, and with a new perspective on how Col. Caldwell had felt while possessed by his Goa'uld.

37. Coup D'etat
A search for a team from Atlantis on an agricultural planet turned up lots of ruins and some bodies. Teyla and Ronon were given the investigation job. Ladon, a Genii defector, offered Atlantis a ZPM in exchange for their help with a coup d'etat. Dr. Beckett found that the bodies with Earther dogtags were imposters, which meant that Major Loren and his team were still alive.
   Ladon says Commander Cowen, the Genii leader, wants to unite the galaxy under his rule using his new atomic weapons. Col. Sheppard contacts Cowen to check up on Ladon. He says the last Wraith cull nearly wiped out the Genii and they're in no position to dominate anyone. So Atlantis offers help with reconstruction.
   Sheppard comes up with a plan to steal the ZPM from Ladon. On the agricultural planet, Teylan and Ronon find photographs of Atlantis personnel with messages promising rewards. Dr. Weir realizes that all of the men carry the Ancient gene, which lets them use Ancient technology. Dr. Beckett says the imposters died of radiation poisoning and only the Genii have that much radioactive material.
   Dr. Weir takes some of Ladon's people prisoner, Sheppard & Co. walk into a trap, the ZPM is dead and worthless and Ladon is working with Cowen, who wants all 10 jumpers from Atlantis or he'll kill his prisoners, starting with Sheppard. Ladon, his chief scientist, is working on a treatment to give the Genii the Ancient gene so that they can fly jumpers. Dr. Beckett finds that he can cure 8/12 prisoners, who are all dying of radiation poisoning.
   Cowen tells Ladon to kill Sheppard after Weir tells him that Ladon's sister is among the prisoners who can be cured. So Ladon stages a coup, releases the Earthers and blows up Cowen and his brigade of followers with a nuke. At the end, Weir offers treatment to all other irradiated Genii.

38. Michael
Lt. Michael Kenmore (Trip Tucker from Star Trek Enterprise) wakes up in the sickbay at Atlantis with amnesia after being captured by the Wraith and rescued. Teyla looks familiar and she pals up with him. Dr. Beckett thinks he can be released but Sheppard gives him an escort. Michael has dreams about the Wraith but the psychiatrist tells him it's just post-traumatic stress. Ronon keeps wanting to fight Michael, who pinches his medical records while Dr. Beckett is asleep.
   Shock horror! 'Michael' is really a Wraith prisoner, who was injected with Dr. Beckett's retrovirus, which zapped his Wraith DNA and let the human DNA take charge, and he got his name from one of the places shown in Dr. Beckett's Classic Scotland calendar. Michael needs a daily shot to keep him human but Col. Sheppard hopes that Beckett will be able to create a biological weapon, which can be released on hive ships and turn all Wraith into humans permanently.
   Michael is not happy about what has been done to him and he does a runner with Ronon in hot pursuit. He kills one of the crew before Ronon catches up with him. There's a big argument over what to do with him and Michael is sent to the Alpha site. There, he takes control of Teyla, makes her his prisoner and escapes through the stargate. Luckily, Teyla scratches the gate address on a handy rock and Sheppard, Ronon and back-up are able to follow.
   They arrive just in time to save Teyla as Michael, now reverting to his Wraith form, is swithering over whether or not to feed from her. The Wraith get 'Michael' back alive and worse, they now know that Atlantis has not been destroyed.

39. Inferno
Sheppard & Co. visit the planet Teranan, where a colony living in an Ancient base has a shield generator which needs fixing. Everything is deep underground and there are earthquakes. The shield is powered by geothermal energy, McKay is teamed up with Narina, the chief scientist and he is horrified when she says the shield has been on continuously for a year instead of only when needed. The base is located in the caldera of a super-volcano, which the power drain has destabilized.
   The Teranans have a hangar containing a big, non-working spaceship. Their Chancellor is reluctant to believe that all life on the planet will be wiped out when the volcano blows, and he thinks the Earthers are after his spaceship, but he accepts an evacuation to Atlantis. After the first group has travelled through the stargate, the one on Teranan is swallowed up by lava. The lack of contact with his planet makes the Chancellor even more suspicious.
   Sheppard tells McKay to fix the ship, which is renamed Orion. Dr. Weir sends Daedalus to continue the evacuation. Col. Caldwell says he'll need 4 round trips, each taking 12 hours. Sheppard wants Orion ready as a 2nd lifeboat. As an added complication, Atlantis detects a Wraith hive ship heading their way, 3 weeks out.
   A group of Teranans decide to take refuge on the surface when they learn that Orion's engines aren't working. A lava flow covers the hangar door above the ship. Teyla and Ronon are trapped on the wrong side of a tunnel collapse but Daedalus beams them up. But the ship can't detect other life signs because the base is shielded. Sheppard finds the base going into emergency lockdown around him but he eventually makes it to the hangar.
   McKay has a plan. He intends to deploy Orion's shield, let the volcano blow the ship into the air and then engage the hyperdrive to escape. To everyone's surprise, the plan works, the Teranans are relocated to another planet and their Chancellor lets Atlantis use Orion. But Dr. Weir thinks it's not going to be enough to tackle a Wraith hive ship.

40. Allies (1)
Daedalus and Orion were waiting to ambush the Wraith hive ship off Atlantis but Michael was aboard and he wanted to talk. His message was that all of the Wraith had emerged from hibernation 2 years before, they were running out of food and civil war had broken out. Michael's plan was to give Dr. Beckett's retrovirus to his hive's enemies to turn them into food. He was also willing to give Dr. Weir information to allow Wraith shield codes to be cracked and let the Earthers transport nukes onto hive ships.
   Under the threat of 'co-operate or we'll tell the rest of the Wraith that Atlantis wasn't destroyed', Dr. Weir accepted the offer. Teyla remained doubtful. She was sure Michael was up to something. The Wraith queen visited Atlantis. The Wraith tested an aerosol of the virus on one of their kind and the queen fed successfully from the humanized Wraith. She set up an attack on another hive ship, but it turned into a battle when the other hive found the canisters of retrovirus.
   McKay got the plans of a hive ship and he was allowed to help repair the battle damage caused by the other hive. McKay & Sheppard came up with an alternative delivery system for the retrovirus and McKay decided he had to be aboard the Wraith ship, with a secret personal transporter, when the system was tested.
   Things started going wrong with the computer on Atlantis. Daedalus was fired on by both Wraith ships, McKay & Ronan were captured because their transporters didn't work and Sheppard's fighter disappeared. There was a virus in the Wraith plans, which had provided the Wraith with the location of every world in the Atlantis databank. And they reckoned their next stop was Earth!

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