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.

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.

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.

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.

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.

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.

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.

The team desperately attempts to stop two Wraith hive ships from reaching Earth. Sheppard must rely on an old foe to rescue McKay and Ronon.

The Atlantis team must decide the fate of a colony of Wraith they have turned into humans. Dr. Weir must defend her leadership when she is evaluated by the I.O.A.

Ronon Dex is captured by the Wraith and returned to his homeworld, where he is haunted by his past as he is forced to once again become their prey.

The Atlantis expedition is stunned to learn that a ship full of Ancients is returning to reclaim their lost city.

The inhabitants of Atlantis begin to suffer ill effects when the planet's whale population begins migrating to the island city, bringing an unexpected harbinger of doom.

With a plan to potentially extinguish the Replicator threat, the Atlantis team must seek an alliance with a fleet of Wraith ships.

As a mysterious new illness sweeps through the Pegasus Galaxy, Teyla is convinced by a vision that the father of her child is trying to communicate with her.

Lt. Colonel John Sheppard and his team are trapped under the rubble of Michael's facility in order to rescue Teyla Emmagan. As Colonel Samantha Carter launches a team to rescue the rescuers, little do they know that Michael Kenmore is also searching the planet for the survivors.

Dr. Daniel Jackson arrives in Atlantis to investigate a hidden lab left behind by the rogue Ancient scientist Janus. Their discovery has attracted the attention of a mysterious group of aliens, who infiltrate the city. Meanwhile, "Todd" and a delegation arrive on the Daedalus to bring forward Dr. Jennifer Keller's gene therapy.

"Todd" informs the Atlantis expedition that a rogue group of Wraith has acquired several Zero Point Modules to power a Super-hive, and wants it destroyed. However, after the Daedalus is disabled, they learn that the ship is heading straight for Earth, and they must stop it before it gets there.