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

Colonel Sheppard and his team embark on a risky mission to steal a Z.P.M

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. 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

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