The team searches for a valuable Zero Point Module rumored to be hidden on the planet Dagan -- but their new allies have motives of their own.

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

Plagued by terrifying nightmares, Teyla begins to recall a time when she and her father were captured by the Wraith and subjected to disturbing experiments.

With a group of Wraith hive ships on the way to Atlantis, the team searches for a place to flee and a way to destroy the city. McKay leads a team to try and activate the Ancients' orbital weapons platform.

All hope seems lost, until Colonel Everett arrives suddenly from Earth. He is determined to defend the city until the arrival of a ZPM, brought by a new ship.

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 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.

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.

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

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 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.

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

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.

Weir and the team visit an advanced civilization that split off from the Lanteans thousands of years ago, but discover that they may not have left Atlantis in peace.

Colonel Sheppard finds himself the prisoner of a Genii commander, along with a desperately hungry Wraith who has been separated from his hive.

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

After an Ancient device gives Rodney superhuman powers, his enhanced brilliance is checked only by his impending death -- unless he can learn how to ascend.

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

The team tries to relax during a mandatory day off, until an explosion leaves three people dead -- and reveals that one scientist is a walking time bomb.

The Atlantis team investigates the disappearance of one of their allies, only to find an old enemy engineering a race of powerful monsters.

An unstoppable energy weapon leaves Atlantis under siege after Earth launches a preemptive attack against a very powerful enemy's homeworld.

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.

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.

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.

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

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.

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.

The Atlantis expedition mysteriously finds the Daedalus, abandoned and drifting in space. When Lt. Colonel John Sheppard's team come to investigate, the ship mysteriously disappears. They soon discover that the ship is actually an alternate Daedalus from a Alternate reality, and the team must find a way back to their Universe or risk being stranded forever in an unfamiliar reality.

While on a mission, Lt. Colonel John Sheppard's team inadvertently brings a mysterious entity to Atlantis. They soon learn that the entity is nothing more than Dr. Elizabeth Weir, who was thought to have been killed after her capture by the Asurans.

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.

While being evaluated by the International Oversight Advisory, Richard Woolsey meets a beautiful scientist new to Atlantis, who is not what she appears. Meanwhile, Lt. Colonel John Sheppard is captured and tortured by an enemy he thought he'd killed several years ago: his sworn enemy, Genii Commander Acastus Kolya.

"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.