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.

A run-in with a Wraith Dart leaves the consciousness of a precocious Atlantis security officer trapped in Dr. McKay's mind.

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.

Colonel Sheppard begins to undergo a disturbing physical transformation after being exposed to Beckett's anti-Wraith drug.

The team is captured by the missing Lieutenant Ford, who is now leading a group of young men who are taking the Wraith enzyme -- and who wants the team's help in a suicide attack against a hive ship.

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.

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.

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.

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.

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.

Sheppard and McKay discover that their competitive video game has been controlling a planet of real people, who now stand on the brink of war.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

Michael Kenmore has infiltrated Atlantis with an army of his Hybrids, and closes off Stargate Operations and the surrounded levels to prevent anyone from taking it back. His plan; take Teyla Emmagan and her child to perfect his Hybrids, and to destroy the base when they're done. Meanwhile, Lt. Colonel John Sheppard, Dr. Rodney McKay and a team try to take back the city before Michael leaves with what he wants.

After a Wraith Hive Ship shows up over Atlantis transmitting a distress call, Lt. Colonel John Sheppard's team discovers that its crew has been stricken with a disease they helped create.

"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.