Lt. Colonel John Sheppard's team is invited by the Coalition of Planets in order to form an alliance. However, the team is misled and is faced to stand trial, for their alleged crimes against the Pegasus galaxy. Their best chance of freedom, is the experiences of Richard Woolsey.

The team finds Lucius Lavin manipulating the people of another hapless planet, using Ancient technology to pose as an invincible hero.

Sheppard's team meets an obnoxious man who is adored by all thanks to a secret that he carries -- and who has an unexpected effect on them.

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.

Elizabeth Weir wakes up in a mental institution, where she is told that the expedition to Atlantis and the Stargate are figments of her imagination.

Sheppard and Ronon are influenced by a mind-altering device created by the Wraith while on a mission to rescue a lost team.

The team finds themselves in mortal danger when their Puddle Jumper ship becomes lodged in the Stargate.

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.

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.

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

Ronon Dex is captured by Tyre, who wants to hand him to the Wraith in order to maintain his role in their circle. However, when the deal turns sour, and Tyre is left for dead, the Atlantis expedition persuade him to take back their friend. Meanwhile, The Wraith turn Ronon into a Wraith worshipper.

Dr. Carson Beckett, now a traveling doctor in Pegasus comes across a planet, where some of the villagers are refugees from Balar, a planet infected with the Hoffan drug, and destroyed by the Wraith. However, the Wraith arrive on the planet and gives the village an ultimatum, hand over the Balarians, or face destruction of the entire civilization.

Dr. Jennifer Keller's body is inadvertently taken over by a cunning thief, Neeva Casol. While Neeva tries to escape Atlantis, Keller finds herself imprisoned with a death sentence on another planet, forcing the team into a race against time to return Keller to her original body before she is put to death.

After a series of run-ins with the Wraith, the team begins to suspect their Athosian allies of having a spy in their midst.

With a brief opportunity to send a data transmission to Earth, members of the Atlantis expedition compose video messages home to their loved ones.

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.

When a mysterious alien organism takes Dr. Jennifer Keller as its host, the newly revived Dr. Carson Beckett and the crew desperately search for a serum to save her from the evolving intruder before it can infiltrate Atlantis. In the meantime, Richard Woolsey officially joins the team, having been chosen as Colonel Samantha Carter's replacement to lead the Atlantis expedition.

Sheppard's team investigates a downed Wraith ship, and find themselves stuck on a planet with a lone Wraith survivor.

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.

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.

The team discovers the last of a civilization in suspended animation, whose survival is at risk when their station is critically damaged.

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

Dr. Carson Beckett is called in to help a team investigating a lab that once belonged to Michael Kenmore. But soon, they realize that a group of experiments that even Michael couldn't control are hellbent on killing the team.

Sheppard tries to convince Weir to mount a rescue mission to free Colonel Sumner, Teyla, and the others captured by the Wraith.

Sheppard and the team visit a world where no one is over 24 years old -- because of a ritual suicide practice they believe keeps the Wraith at bay.