Атлантис е спасен в последния момент от Дедал, който успява да унищожи останалите два корабa кошери. Въпреки това, още 12 са на път и те бързо се адаптират към мерките на Таури. МакКей и екипа му трябва да инсталират новият МНТ и да повишат щитовете на града, за да защитят Атлантис, преди останалата част от Призрачният флот да пристигне и да превземе града. Междувременно, екипът намира и лейтенант Ейдън Форд, който е получил предозиране от ензима на един рейфовете.

След двупосочно пътуване от Земята обратно към Лантеа, необяснима смърт се случва на борда на Дедал. Един човек е бил убит, когато разбират че за смърта му е отговорен компютърен вирус на Призраците, който се е качил в компютрите Дедал и взима контрол върху кораба. Д-р МакКей и екипа му трябва да го спрат. По време на срещата в Старгейт, д-р Уиър научава, че Пентагонът планира да замени Шепард с полковник Колдуел.

След намиране на мъртъв Призрак на P3M-736, експедицията на Атлантис намира доказателства, че лейтенант Ейдън Форд е отговорен за това. Шепърд и опитният му екип се опитват да открият лейтенанта, само че се озоват в плен на един млад човек, който е преследван от Призраците.

След като МакКей и лейтенант Лаура Кадмън са заловени от Призрачна стрела, екипа на Шепърд свалят стрелата. Опитвайки се отново да материализират двойката, съзнанието на лейтенант Лаура Кадмън се озовава в тялото на Маккей и го споделят и двамата. Ронън Декс през това време решава дали да остане в Атлантис.

Екипа на Шепард открива планета недокосната от Призраците, защото правителството изпраща своите престъпници в наказателен остров, където Призраците могат да се хранят. Джъмпера на Шепард е свален и се разбива на острова.

Екипът намира пост на необитаема планета и откриват, че древните са изследвали източник на захранване, пред който МНТ-то изглежда като малка батерийка. МакКей веднага изследва източникът на енергия и излага Атлантис на риск, когато се опитва да изключи тайният древен източник на захранване. Междувременно, Ронън Декс научава, че една малка част от хората му са оцелели след атаката на Призраците на планета му, включително и бившия си военен треньор, с когото той има недовършена работа.

The team discovers a young Wraith girl who has been raised by a human, and is in hiding from the people of her human village in fear of her life.

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

When the team finds an Ancient warship adrift on the edge of the galaxy, its crew still alive, Colonel Sheppard enters their virtual reality stasis to communicate with them.

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.

Sheppard finds himself on a planet where time passes more rapidly, with no way to contact his team or return to Atlantis.

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.

When Dr. McKay is trapped underwater in a sinking Puddle Jumper, his only chance for survival may be an hallucination of Samantha Carter.

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.

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.

An amnesiac young Lieutenant in Atlantis suffers from disturbing nightmares that he is a Wraith, only to make a shocking discovery about himself.

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 team desperately attempts to stop two Wraith hive ships from reaching Earth. Sheppard must rely on an old foe to rescue McKay and Ronon.

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.

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.

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

Rodney McKay is reunited with his estranged sister back on Earth, who has given up a brilliant career as a scientist to raise a family.

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

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

The Atlantis team goes against orders to try and save Atlantis from Replicator control -- and to rescue General O'Neill and Richard Woolsey, who are trapped in the occupied city.

The inhabitants of Atlantis begin to suffer ill effects when the planet's whale population begins migrating to the island city, bringing an unexpected harbinger of doom.

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

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.

The team discovers an Ancient drilling station deep beneath the surface of the ocean, only to find that a Wraith queen is still alive there.

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.

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. 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.

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.

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.

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.

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. Rodney McKay is infected with the Pegasus equivalent of Alzheimer's disease, known as Second Childhood, a common illness among the elderly in the galaxy. The only way to save him is a shrine on Talus. The downside is that it has turned into a Wraith outpost.

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.

The Atlantis expedition has a plan to remove the Wraith's dependence on feeding to use an experimental gene therapy from Michael's database. However, in order to convince the Primary, the Wraith leader, Teyla Emmagan must pose as a Hive Queen.

Dr. Jennifer Keller is kidnapped by a runner named Kiryk. While Dr. Rodney McKay and Ronon Dex tracks them, Kiryk takes Keller to a seriously injured young girl. She must do it fast, since the Wraith have found him, and are hunting them down.

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.

As Dr. Rodney McKay and Dr. Daniel Jackson is held prisoner by the Vanir, they make a startling discovery about who they really are. Meanwhile, "Todd" and his Wraith hijack the Daedalus to find and destroy those who activated the Attero device. The Travelers arrive and Lt. Colonel John Sheppard must help them get to the planet before "Todd" uncovers a way to discover the device for good, even if it means sacrificing McKay and Jackson's lives to do so.

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.

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.

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.

Dr. Rodney McKay reluctantly returns to Earth to witness the triumph of his rival Dr. Malcolm Tunney, but must help shut down a deadly weather device when the new technology goes horribly awry.

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.

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.

In the city of Las Vegas in an alternate reality, police Detective John Sheppard investigates a series of bizarre murders where each body appears to have desiccated. He is soon called to Area 51, where Dr. Rodney McKay explains the situation.

"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.