Floating in deep space with the city's protective shield failing, the team must do all they can to keep Atlantis alive. Meanwhile, a radical injury threatens Dr. Weir's life.

Colonel Sheppard and his team embark on a risky mission to steal a Z.P.M. power module from the Replicators – but must rely on a compromised Dr. Weir to succeed.

When a group of Ronon's people enlist the team's help in raiding a Wraith weapons facility, Ronon reconsiders whether his future lies in Atlantis or with his friends.

During an off-world mission Colonel Sheppard unknowingly becomes host to an alien entity, which infects others in Atlantis and afflicts them with terrifying nightmares.

Colonel Sheppard is captured by the inhabitants of a generational ship and their beautiful leader, who wish to use his ability to use Ancient technology for their own ends.

When a virus causes amnesia in everyone except Teyla and Ronon, the Atlantis team must work together to find a cure before their memories fade entirely.

During a visit to New Athos, Teyla and Dr. Keller find themselves on the run from a primitive tribe of warriors.

The team meets a man with extraordinary prophetic abilities, who gives them a dark prediction about Atlantis's future. Meanwhile, the Wraith seek a new alliance with Atlantis in their war with the Replicators.

Rodney McKay goes in search of his sister on Earth after she is kidnapped by the head of a powerful corporation.

A mysterious drone crashes into Atlantis, indicating that the Replicators may have found the city. But when Elizabeth Weir appears, the team realizes that the probe is just a part of a bigger mystery.

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

The team finds their former Wraith ally's hive ship drifting in space, which leads them to a secret project that could turn the tide of a civil war.

An automated lockdown traps Atlantis personnel in various parts of the city, each of them hoping the others will come to their rescue.

Colonel Sheppard and Dr. McKay must protect a child princess on a pilgrimage before she can become queen, and learn that she has dangerous enemies threatening her life.

While on personal leave on Earth, Sheppard and Ronon learn that scientists have engineered a human-form Replicator – who is now on the loose.

McKay, Carter, and Keller are trapped in an underground chamber while on an off-world mission, with no apparent means of escape.

Teal'c visits Atlantis to counsel a headstrong Ronon, who is up for review by the I.O.A. But the two must work together when the Wraith invade the Midway space station in order to reach Earth.

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.

The team is shocked when an old friend, believed to be dead, miraculously returns to them. Teyla plans an escape from Michael's captivity.

Sheppard returns to Atlantis after a mission and finds the city abandoned, all systems dead – and instead of ocean, sand dunes as far as the eye can see.