Daniel decodes the gate setting for Atlantis, in the Pegasus galaxy. It takes the full strength of the ZPD power source to dial through, and Dr Weir takes a large expedition through, all knowing they may never get back, unless they can find a ZPD there to dial home. They find themselves in a well preserved city, hundreds of feet under the sea. A recording from the Ancients says they were defeated by a powerful enemy, and fled back to Earth. The ZPD power source in the city is nearly drained, and when it fails, the city will be crushed by the sea. A team goes on a local gate trip to find another safe place. They find a small village of humans hiding from the Wraith. The Wraith arrive, and abduct the Colonel and some villagers. Major Sheppard mounts a rescue mission. The Colonel dies, and a multitude of Wraith are released from hibernation, but the villagers are saved. As the power for the shields finally fails, Atlantis rises from beneath the waves. The exploration team and the rescued villagers form a new community.
One of the children plays hide and seek, and discovered a transporter system that takes them to a science lab, where they accidentally release a dark entity that eats energy. Meanwhile, gene therapy has allowed Dr McKay,one of the scientists to use Ancient technology, and he's found a personal shield that makes him invulnerable, but he can't seem to switch it off. The team try to lure the creature back into its holding cage, but it refuses, so they trick it to go through the wormhole.
The puddle-jumper gets wedged halfway through the wormhole, and with Major Sheppard injured by a Wraith neck-biter creature, the rest of the crew and Atlantis base have only 38 minutes to solve the problem before the wormhole shuts off, cutting the ship in half and killing everyone on board.
The away teams keep getting attacked by Wraith on their missions. It seems there may be a spy amongst the Elosians. New security measures antagonise them. When land is discovered on the Atlantis planet, they elect to leave and set up home there. Eventually it is discovered that Teyla's locket is unknowingly a Wraith tracking device. They use this to capture a Wraith.
The away team find a village of children, who all sacrifice themselves at 25, to stop the Wraith returning. But Dr McKay discovers a ZPG is powering a shield keeping them away. When he turns it off, a Wraith bracelet starts transmitting...
The Atlantean team discover a planet whose inhabitants are working on a vaccine against the Wraith, and help them. A terminally ill volunteer agrees to test it. The captive Wraith not only can't feed on him, it dies. The Atlanteans realise this will cause the Wraith to utterly destroy the planet once they discover that it is a weapon. Nevertheless, the inhabitants start a programme of mass vaccination -- and continue it, even after they discover it is fatal half the time.
Dr McKay finds a Gate that is powered by a mysterious planetwide energy source, sufficient to open a wormhole back to Earth. They decide to use it to report back, but not to travel home, since there would be no way to return. Once it is open, they are informed that Prometheus is available to return them, so Weir, Sheppard, McKay, Teyla, and Ford decide to visit. However, once back, there are stronger and stronger doubts: the Pentagon is worried by the Wraith, the Prometheus is damaged, the Asgard aren't available to help. Eventually, enough discrepancies arise that they become suspicious, and demand to know what's happening. They are actually still back on the original planet, living out scenarios, because the power source is actually non-corporeal lifeforms, and opening the Gate would kill millions. The team persuade the beings that, despite their desire to go home, they would not do so at that price. So they are allowed to return to Atlantis.
Atlantis is running out of food, so Teyla takes the team to an Amish-like Genii, to barter. But their seemingly peaceful lifestyle is a facade for a military programme into building an atom bomb to destroy the Wraith. The people are dismayed to hear the Wraith are wakening early. A joint mission to gather more intel leaves one of the Genii dead, and the rest demanding the retention of the Puddlejumper. But Sheppard out-bluffs them. However, another potential allay ends up as an enemy.
Sheppard and Teyla discover that a giant storm is about to hit Atlantis. McKay contrives a plan to use lightening to repower the shield, but it's chancy, so Weir orders an evacuation. The planet where they go betrays them to the Genii, who invade, and take over Atlantis, holding Weir and McKay hostage. Sheppard is loose, and the Genii Commander threatens to shoot Dr Weir if he does not surrender...
McKay persuades the Genii Commander not to kill Weir, but Sheppard thinks she is dead, and goes all "Die Hard". He raises the Stargate shield as reinforcements are coming through, killing about 60 Genii. In a bluff, McKay manages to persuade the Commander that the shield cannot be repowered, so he has to evacuate. He tries to take McKay and Weir with him, but Sheppard rescues them. McKay raises the shield at the last moment. They have their city back, but the Genii have even greater reason to hate them.
Sheppard, McKay and two other scientists are investigating an Atlantean battle satellite when they hear a faint Wraith distress call from the planet below. Investigating, they discover a 10,000 year old Wraith ship, and one Wraith left alive. It captures their Puddlejumper, and Sheppard must play a deadly game to win it back.
While checking Atlantis for storm damage, some personnel die of a brain aneurysm. McKay orders a quarantine lockdown. They discover a nano-virus that kills humans without the Ancient gene in six hours. Sheppard sets off a naquada generator in the atmosphere, causing an EMP that destroys the nanites.
The team are attacked by Wraith ships around a new planet when a large energy bolt destroys the attackers. They go down to the planet and discover an idyllic pastoral paradise, whose people have never heard of the Wraith. The team ask if other refugees can come to live there, but the high priestess says their protector won't allow it. In order to try to persuade her further, they invite her back to Atlantis. There they discover she is in fact an Ancient who refused to leave her planet to the Wraith, and is being punished by being required to protect them, and no-one else.
In a remote part of Atlantis the team discover an aged woman who has been in stasis for 10,000 years. They wake her, and she claims to be Dr Weir, flung back in time from the first, disastrous arrival at Atlantis, when everyone drowned under the sea. She and an Atlantean called Janus changed enough of the past so that this time around it was more successful, and she also has the gate addresses of the location of five ZPMs.
The team follow up one of the ZPM gate addresses, and find a society that worships the device. They discover its location, but the Genii are watching them, and attempt to take it. They don't succeed, but the natives take it to hide, awaiting the "true" Ancients to return. Meanwhile, Atlantis is scanned by a Wraith scout, and three Wraith hive ships are discovered only two weeks away.
Shepard and Teyla go to see what the Wraith are doing. The rest of Atlantis prepare to send private messages back home, packed into a 1.3 second burst transmission. the Wraith news is bad: each hive ship is accompanied by destroyers and hundreds of scouts. This may be the end.
Teyla is plagued by nightmares of the Wraith. She learns that she has the gift of sensing the Wraith because she is the descendent of some human genetic experimental subjects of a rogue Wraith -- and she also has the ability to hear their thoughts. Unfortunately, when she does, she is possessed by a Wraith. The evacuation site is compromised. She also learns that the Wraith have awakened too soon, and there is not enough food for them, so they are coming to Atlantis to find a route to a new rich feeding ground: Earth.
The Atlantis team desperately search for a new Alpha site for possible evacuation. McKay and a team goes to repair the Ancient satellite [ 1.12. The Defiant One ] . A soldier is attacked, and the forensic exam shows Wraith DNA: the pilot of the Wraith scout ship [ 1.16. The Brotherhood ] has been on Atlantis for the last fortnight. The team prepare a self-destruct sequence to destroy Atlantis and wipe the Ancient database to stop it falling into the hands of the Wraith, even though they will be able to take only 10% of the data with them. McKay gets the satellite working by jury-rigging the power conduits. It destroys one hive ship, but then stops working, and is destroyed. Dr Weir gives the order to evacuate...
... but a team from Earth arrive to help. The gate opening has been powered by a newly discovered ZPM, which is now being used to power the Daedalus, which will be with them in 4 days. But the specially deployed Naquada-enhanced nukes are taken out by small asteroids, and the Wraith attack. They also beam in and overrun the city. Weir negotiates with the Genii for two of their nukes. They are put into Puddlejumpers to be flown on autopilot into the hive ships. But the autopilot stops working, so Shepard takes flies one himself...