Atlantis continues to defend itself against a massive Wraith attack. While treating Lieutenant Ford, Dr Beckett begins to worry about whether Ford has been infected with a Wraith enzyme that could prove permanently damaging.
The Daedalus' computer becomes infected by a Wraith virus, and Dr McKay and his team must try and knock it out as a team of Atlantis explorers returns. Meanwhile, Dr Weir learns of the SGC's plan to lose Major Sheppard and bring in Colonel Caldwell.
Sheppard and the team look for a missing Lieutenant Ford, but soon find themselves prisoners of a man who is on the run from the Wraith.
Lt Cadman's consciousness is inadvertently transferred into Dr McKay's body during a technical malfunction.
Sheppard and the team come across a planet where the natives are left alone by the Wraith and only the criminals sent to an island penal colony become food for the Wraith. Danger lurks for the team, however, when its jumper is forced down onto the island by the island's leader and is in need of repairs.
Ronon Dex learns that many of his people survived a planetary attack by the Wraith and looks to settle a score with his old military mentor. Meanwhile, McKay's interest in an ancient power source may have dire consequences for the safety of Atlantis.
Dr Beckett experiments with a self-made virus that will change Wraith forms into those of humans, but his testing may put Sheppard's life in danger.
The team must hurry to find a cure for Sheppard after an attack leaves him with an injury that will change him into a Wraith.
The team comes across a decrepit ship called Aurora, which turns out to be inhabited by Ancients.
The team tracks down Lieutenant Ford, now leading a renegade band whose mutated bodies have been embedded with Wraith DNA. He tries to get Sheppard and the team to help him take on a dangerous hive ship.
Sheppard becomes a prisoner of the Wraith, as Ford attempts to force a hive ship on the defense.
Sheppard gets stranded on a planet without contact with the team or a way to get back to Atlantis. He soon discovers that time moves faster than normal in this world.
An Earth resident becomes the subject of scrutiny when the Wraith suddenly is clued into the location of Atlantis. When the threat is found to be the Goa'uld itself, Sheppard and the team must try and sort out the human and Goa'uld conspirators who plan to set off a bomb.
Dr. McKay finds himself stuck underwater in a puddle jumper, and Samantha Carter is his last hope for a safe escape.
When the team stumbles upon a world which utilizes antiquated weaponry, Colonel Sheppard becomes caught up in two possible rulers' attempts to seize power.
When two hostile aliens infiltrate the minds of Sheppard and Weir and take control, the two become a danger to Atlantis.
The team comes upon a village and discovers that it has been ravaged by attack. A conflict quickly arises with the Genii, who have taken Sheppard prisoner and usurped control of multiple puddle jumpers.
A lieutenant grappling with memories of his past learns that he was once a Wraith before being loaded with a drug designed by Dr. Beckett.
The team finds itself at the mercy of a planet's volatile volcano.
Atlantis finds itself teaming with a very unusual ally as it continues to battle the Wraith.