Earth's new battlecruiser Daedalus arrives under the command of Colonel Caldwell and saves Major Sheppard from his suicide run on the Wraith Hive ships. McKay and his team must get the new ZPM installed and raise the city shields to protect Atlantis before the rest of the Wraith fleet arrive to take the city.
Daedalus is infected by a Wraith computer virus. Dr McKay and his team must stop it as members of the Atlantis expedition return from Earth after a meeting at the SGC thanks to the ZPM. During the meeting at the SGC, Dr. Weir learns that the Pentagon plans to replace Major Sheppard with Colonel Caldwell.
Sheppard and his team attempt to locate Lieutenant Ford, only to find themselves held captive by a young man who is being hunted by the Wraith.
After McKay and Lt. Laura Cadman are culled by a Wraith dart, Sheppard's team shoots it down. After attempting to re-materialize the pair, Lt. Cadman's mind ends up sharing McKay's body.
Sheppard's team discovers a planet untouched by the Wraith because the government sends their criminals to a penal island for the Wraith to feed upon. Sheppard's Jumper is shot down and crashes on the island.
Ronon Dex discovers that a small number of his people survived the Wraith attack on his planet, including his former military trainer, with whom he has unfinished business. Meanwhile, McKay puts Atlantis at risk when he tries to unlock the secrets of an Ancient power source.
During a mission, Sheppard and his team learn that a lone Wraith -- whose dart had crashed leaving him unable to get to the spacegate -- has been terrorizing a village for some ten years. They offer to help, but soon after they begin to hunt, Teyla senses that something is different about this Wraith.
After being infected by a retrovirus, Sheppard's body begins mutating into something insect-like. Beckett and the team race to find a cure before the mutation has gone too far.
The team finds a large Ancient Ship called Aurora adrift on the edge of the galaxy and it still has Ancients living on board.
The team is captured by Lt. Ford, who is now leading a renegade band that is taking the Wraith enzyme. He tries to get Sheppard and the team to help him take out a Wraith hive ship.
McKay attempts to rescue Sheppard, Teyla and Ronon from the Wraith hive ship that Ford wanted to sabotage and destroy.
Colonel Sheppard is separated from his team while investigating an Ancient device; he finds himself in a domain where time is dilated, progressing faster than normal. Doctor McKay frantically looks for a way to save Sheppard before time runs out!
SGC discover that The Trust has placed a bomb in Atlantis that will go off when Atlantis dials Earth. Daedalus must warn Atlantis and the team must find the traitor in their midst.
Dr. McKay is trapped underwater in a sinking Puddle Jumper and he must rely on Samantha Carter for his survival.
The team discovers an exact replica of Atlantis on a planet they are exploring. The planet is protected by The Protector who uses the technology to keep the villagers in line and the Wraith away. The Protector is dying and Sheppard is caught up in a dispute among the heirs of the throne.
Alien combatants look to settle an ancient score by using Weir and Sheppard as pawns.
When the Atlantis team finds out that the Genii have grown into a new menace, they realize that the armistice with their old enemy may soon come to an end.
Lieutenant Michael Kenmore, suffering amnesia, suspects that Atlantis personnel are lying to him about what actually happened to him on his last mission against the Wraith.
Dr. McKay must save the team when they are caught on a planet with a super-volcano and there is no visible way out.
Atlantis joins forces with a Wraith faction led by Michael, the Wraith they tried to turn into a human, who seeks their help in destroying their common enemies.