A new Stargate team travels to the newly discovered city of Atlantis in the Pegasus Galaxy, in which a primitive human colony is being overun by a tyrannical race of aliens known as the Wraith.
The crew begins to explore Atlantis, but when an alien creature inadvertently gains entrance inside the city, the base, as well as the city's entire power supply, is in jeopardy.
The Atlantis team finds itself in jeopardy when its jumper gets trapped within the Stargate.
Relationships are frayed when the Athosians are accused of providing a haven for a spy.
The Atlantis team find a tribe of children who practice ritual suicide.
The team explores the effects of a new drug that might have the ability to keep the ravenous Wraiths at bay from humans.
The team heads to the planet Gengii to barter for food supplies, but soon find the seemingly quiet farming community that inhabits it is actually developing a potent weapon to use against the Wraith.
The team figures out a way that it can utilize the unique properties of their atmosphere to get back to Earth, but this means the members might never be able to come back to Atlantis.
The city of Atlantis is forced to evacuate when it comes in the path of a powerful hurricane, but the inhabitants are quickly kidnapped by the Genii, along with the McKay and Weir, which prompts Sheppard to figure out how to outmaneuver the Genii.
In the midst of a violent storm that wreaks havoc on the city, the Genii seize the opportunity to capture the evacuated area, but Sheppard is forced to outwit them singlehandedly when Weir and McKay are captured.
When Sheppard and his team answer the distress call of a stranded Wraith ship, they find themselves stuck on a planet at the mercy of a ravenous surviving Wraith.
A deadly virus threatens to devastate the city of Atlantis, and McKay must figure out a way to stop its spread.
The Atlantis team stumbles upon a primitive world that has been unscathed by Wraith attacks and tries to barter with its inhabitants in order to transfer the Atlantis victims of Wraith attacks into its safe confines.
When a woman is discovered in a suspended state in Atlantis, the team learns that it is, in fact, Dr Weir, who has traveled 10,000 years into Atlantis' past.
When the team tries to utilize a module from the planet Dagan, a device which could shield Atlantis from further Wraith attacks, the discovery of a secret brotherhood among the planet convinces everyone that Dagan might be leading the city into the clutches of the Genii.
The members of the Atlantis team prep themselves for a major showdown with the Wraith and compose video messages for their family and friends when a small window of opportunity allows them to transmit information back to Earth.
The team begins to feel the weight of their oncoming battle. Meanwhile, after experiencing a series of horrific nightmares, Teyla comes to learn through her grandmother that her ancestors were victims of Wraith experimentation.
As the Wraith make their approach towards Atlantis, the team tries to figure out how to best evacuate the inhabitants and protect the city. Meanwhile, McKay makes a last ditch attempt to reactivate the weapons of the Ancients.
Earth dispatches a reinforcement stronghold to oversee and protect Atlantis as the Wraith attack draws nearer.