The Daedalus arrives to defend Atlantis from the Wraith onslaught, but it may not be enough when the team discovers that an even larger armada is on the way.

The Daedalus is infected by a Wraith computer virus, while members of the expedition hope to return to Earth.

Sheppard and his team attempt to locate Lieutenant Ford, only to find themselves captives of a former soldier who is being hunted by the Wraith.

A run-in with a Wraith Dart leaves the consciousness of a precocious Atlantis security officer trapped in Dr. McKay's mind.

The Atlantis team finds a culture that lives in relative safety from the Wraith, because they hand over their criminals to the Wraith – and crash-land in the volatile penal colony.

McKay puts the team at risk when he tries to perfect unfinished Ancient technology that wiped out a civilization. Ronon Dex discovers that he is not the lone survivor from his world.

The team discovers a young Wraith girl who has been raised by a human, and is in hiding from the people of her human village in fear of her life.

Colonel Sheppard begins to undergo a disturbing physical transformation after being exposed to Beckett's anti-Wraith drug.

When the team finds an Ancient warship adrift on the edge of the galaxy, its crew still alive, Colonel Sheppard enters their virtual reality stasis to communicate with them.

The team is captured by the missing Lieutenant Ford, who is now leading a group of young men who are taking the Wraith enzyme – and who wants the team's help in a suicide attack against a hive ship.

Colonel Sheppard and his team find themselves prisoners of the Wraith following Ford's attack on a hive ship. Dr. McKay goes to great lengths to help them.

Sheppard finds himself on a planet where time passes more rapidly, with no way to contact his team or return to Atlantis.

When an operative of the Trust plants a bomb in Atlantis, the team must find a spy within their own ranks before the Wraith arrive and discover the city.

When Dr. McKay is trapped underwater in a sinking Puddle Jumper, his only chance for survival may be an hallucination of Samantha Carter.

The team finds a world that possesses Ancient defense technology, where Colonel Sheppard finds himself a pawn in the rivalry between the heirs to the throne.

The team discovers two pods that contain the minds of alien beings, who take control of Weir and Sheppard's bodies to continue their personal war.

After a team from Atlantis goes missing, the expedition finds itself in the middle of a Genii coup.

An amnesiac young Lieutenant in Atlantis suffers from disturbing nightmares that he is a Wraith, only to make a shocking discovery about himself.

Sheppard's team meets a civilization about to be destroyed by a super-volcano, and is trapped there when the Stargate is destroyed during the evacuation.

Michael and his Wraith faction arrive at Atlantis to propose an alliance, hoping to use the retrovirus to transform their Wraith enemies into prey.