A team of scientists think they have found the location of the long lost city of Atlantis. It can be reached by a Stargate address that leads to the Pegasus galaxy.

Rodney can't remove an Ancient device that makes him invincible but prevents him from eating or drinking. Meanwhile, there are power malfunctions throughout the city and one of the Athosians mentions seeing a shadow.

Sheppard gets bitten by a Wraith-like bug and is dying. While the puddle jumper returns, it gets stuck in the Stargate. There's 38 minutes to find a solution.

There's suspicion of a Wraith collaborator and some of the team suspect the Athosians. Ford and Sheppard find land on Atlantis' planet.

Atlantis offers help to the Hoffans, who are working on a defense against the Wraith.

Two hurricanes are approaching Atlantis and an evacuation is necessary. The leader of the planet taking them in tells the Genii about the situation.

McKay and Weir start repairing the grounding station, while Sheppard tries to fight Kolya. The puddle jumper on the mainland enters the eye of the storm.

A team of scientists, including McKay, Zelenka and Ford, are exposed to a deadly virus. Sheppard goes after one of the scientists trying to escape.

Sheppard invites a priestess, who claims to not know about a weapon protecting her planet from the Wraith, to Atlantis to discuss asylum for refugees.

It's Elizabeth's birthday and she gets a very special gift: a woman who has been in stasis in an Atlantis' laboratory for 10,000 years and is actually herself.

The team is on Dagan, where they must find key stones to retrieve a ZPM. Zelenka finds out Atlantis has a deep space scanner.

McKay finds a way to send a message to Earth, leaving space for personal messages. Sheppard and Teyla are off to spy on the Wraith fleet approaching Atlantis.

Teyla is haunted by nightmares, leaving her agitated. After seeing a psychologist, an old Athosian woman tells her a secret about her ability to sense the Wraith.

McKay and Zelenka come up with a plan to repair the Ancients' weapon satellite. Bates and Teyla get into a fight. He is found unconscious and badly injured shortly afterwards.

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 and the two hive ships are destroyed. Atlantis seems saved, then Zelenka detects 12 more ships. Ford seems changed after a fall in the water.

McKay, Sheppard, Beckett and Weir are on the Daedalus. McKay finds a Wraith virus that is infecting ship systems and sending a signal to the Wraith.

The team is searching for Ford on a planet. Teyla and Sheppard are taken hostage by a stranger, while Ford tries to convince McKay that he's normal.

After an attempt to retrieve McKay and Lt. Laura Cadman from the memory banks of a Wraith dart, Cadman gets stuck in McKay's mind.

The team discovers a planet where the Stargate is kept on a prison island to keep the Wraith satisfied. Their magistrate is willing to trade a rare mineral.

The team discover an Ancient project to create the ultimate power source. McKay thinks he can finish it. Ronon finds out he is not the only surviving Satedan.

The team find a hidden Wraith girl, cared for by a man with a serum that he claims can satisfy her hunger. Beckett wants to perfect a retrovirus that can turn Wraith into humans.

Sheppard is infected with the Wraith retrovirus and slowly turns into an Iratus bug. To provide a treatment, stem cells must be retrieved from one of their eggs.

McKay finds an Ancient warship adrift in space. Sheppard finds out they are carrying a communique that mentions a weakness in Wraith technology.

The team is captured by Ford and are forced to take the Wraith enzyme. Ford has a plan.

Sheppard's interrogation is suddenly aborted. Teyla senses another hive ship has arrived. Meanwhile McKay tries to convince his guard to call in help.

The teams discovers a ridge that can only be entered through a door. Sheppard gets pulled in by a field. McKay discovers time goes very fast behind it.

The Trust, a Goa'uld terrorist organization, has planted a bomb in Atlantis.

McKay and a pilot crash with a puddle jumper into the ocean on Atlantis. They start to sink.

Colonel Sheppard's team finds a world where the leader lives in a tower that possesses the power to stop Wraith attacks.

The team discovers two life pods with a dying woman and man in it. Upon opening Weir gets imprinted with the mind of the woman. She asks a special favor.

While Teyla and Ronon investigate the mysterious death of Major Lorne, the Genii Ladon Radim contacts Atlantis. He wants to trade a ZPM for weapons supplies.

Michael Kenmore, a new lieutenant, awakes in the infirmary and doesn't remember a thing. The other expedition members are very concerned about his well-being as he seems different.

Atlantis helps with repairing an Ancient shield generator on Taranis. They discover the Taranians are in possession of an Ancient warship.

The hive ship approaching Atlantis is Michael's. He wants a trade: the retrovirus for not revealing the secret of Atlantis and insights on Wraith technology.

Fallen into the Wraith trap, McKay initially resigns to fatal captivity in a cocoon, but Ronon keeps struggling to attempt escaping, or at least taking some Wraith down with them. Sheppard managed to hide his glider on the very hive ship, seeking a way out, surprised to get radio contact with Michael, who seeks revenge after the ingrate queen has him semi-restrained as 'too human' suspect. While they try to sabotage the hive and maybe escape, the Daedalus and Orion race just in time to fight the two hive ships before they may attack earth. Weir is summoned to SGC for a pointless grilling by the International Oversight Advisory, finding them bureaucrats unable to risk a decision beyond questioning what was already done. So she returns, never mind the career risk compared to a Wraith culling. Sheppard manages to reach the Daedalus and his party comes up with a daring plan to overpower the hive with the weaponized retrovirus, despite bombarded damage compromising even their life-support systems.

Sheppard and the others are now in control of the one remaining hive ship with most of the Wraith transformed into human form, courtesy of the retrovirus. They do learn something interesting about female Wraiths, however. After they return to Atlantis, the question becomes one of what to do with the Wraiths who are again human, especially Michael who has proved to be quite helpful. Elizabeth Weir meanwhile is surprised to hear that she is to return to Atlantis as the expedition leader. She will be accompanied however by Richard Woolsey who is to review her leadership and make recommendations to the International Oversight Advisory on whether she should be allowed to continue.

Sheppard and the team continue their visits to new planets. McKay is tired of all these visits and is keen on implementing a series of gates that will allow them to travel from Atlantis to Earth in a mere 30 minutes without using the power of a ZPM or the two weeks it takes them on the Daedalus. He takes a somewhat different tack however when he sees all of the very friendly young women in the village. Their leader, Lucius Lavin, seems to be a very affable sort and has the locals eating out of their hands. He claims to be an apothecary of sorts and have a cure for every disease, which is certainly of interest to Dr. Beckett. Lavin is invited to Atlantis and soon everyone, including Elizabeth Weir and McKay have fallen victim to his charms. It's left to Sheppard to sort it all out.

After a group of people capture and give Ronon to the Wraith, he becomes a runner again, but this time he's left in his home planet, Sateda, where the Stargate has been disabled.

The Atlantis expedition encounters a highly advanced race, the Asurans. They initially believe them to be the Ancients. However, this new race is just a new face of an old nemesis.

Dr Weir finds herself on Earth where, to everyone else, the Atlantis Expedition was just her delusion.

John Sheppard is kidnapped by the Genii and is in the company of a Wraith.

Rodney's sister is brought to Atlantis to make use of one of her theories.

A device that creates hallucinations affects the team off-world.

The Atlantis expedition must turn to an old friend for help as the Asurans prepare to invade the city.

The team returns to Atlantis in an attempt to regain control of the city.

Teyla witnesses what appear to be an Ancient apparitions, which soon other people start to see.

The team investigate rumours of an invincible hero off-world, only to find Lucius Lavin again manipulating a hapless village.

When Rodney uses an Ancient device, he gets special powers, but soon Dr Weir discovers it's a double-handled gift: if he doesn't ascend, he'll die.

The Atlantis team finds a program in the Atlantis database which throws Mckay and Sheppard into a Simsesque game that could destroy two civilizations in the Pegasus Galaxy.

The team boards a crippled space station to discover people have been preserved there with the hope to outlive their enemy, the Wraith.

With everyone having a Sunday off - something recommended by psychologist Dr. Heightmeyer - all of the members of the Atlantis team pursue leisure activities. Rodney McKay and Carson Beckett are scheduled to go fishing; Sheppard decides to teach Ronon Dex about golf; Teyla spends some time in the gym; and Elizabeth Weir has a lunch date with the handsome Mike Branton. Their day off however is interrupted by a powerful explosion near the mess hall killing and injuring several members of the team. McKay thinks he knows the cause of the problem - a device found by two junior members of his team may have turned some of them into walking time bombs by creating explosive tumors in them.

The Atlantis team finds an Ancient underwater research facility and puts a team together to check it out.

After losing contact with the new Taranin (the people rescued by the Atlantis team when a super volcano threatened to destroy their planet) settlement, Sheppard's team leaves to investigate. Finding the town deserted, they move to investigate an extensive subterranean tunnel system. What they find there holds dark tidings for the entire Pegasus Galaxy.

After learning the Asurians are building a fleet of ships, Earth sends its newest ship, the Apollo, under the command of Colonel Abe Ellis to initiate a preemptive first strike to stop them from attacking Atlantis or worse, Earth itself.

A plague of sorts is spreading across the Pegasus galaxy and Dr. Keller estimates that hundreds of thousands will die if they don't don't find a way to stop it. Her research shows however that the disease's origin is with the Hoff, who had been working on a way to kill the Wraith. Sheppard and the others think they know who might be spreading the virus and why. Teyla meanwhile believes she is receiving messages from Kanaan, the father of her child. She's getting his messages while sleeping and most think she's just dreaming. She follows the clues he gives her but she is taken prisoner by an old enemy who has very specific plans for her. In their search for Teyla however, Sheppard and McKay find someone completely unexpected.

Slowly, everyone on Atlantis comes to terms with the sudden re-appearance of Dr. Carson Beckett who, he claims, has been Michael's prisoner for some two years. He tells them what he was doing in Michael's laboratory and they set off to find the kidnapped Teyla. Dr. Keller figures out just how he's come to there at all. Sheppard meanwhile has been using all of his contacts to try and locate Teyla but they come across someone from the past. Teyla in turn has found some of the Athosians alive but they are few in number as a result of Michael's experiments. Michael explains to her just what it is he wants from her as well as his own plans for the future.

Dr. Carson Beckett is removed from stasis because he's the only one who can find the antidote to a mysterious virus that has incapacitated base personnel, beginning with Dr. Jennifer Keller.

Sheppard and Beckett battle zombie-like, Wraith-engineered mutants with a team of the best and brightest female SG members.

The Atlantis team endeavors to thwart Wraith plans to either find a cure for the Hoffan drug (which makes humans deadly to Wraith feeding on them) or exterminate all those infected.

Sheppard and his team are lured to a planet and are soon put on trial for crimes against the people of the Pegasus galaxy. In flashbacks, the three judge tribunal recounts the indictment against them including the re-awakening of the Wraith and the various missions where at least a few, if not more, innocent bystanders were killed. Sheppard does his best to argue that on balance, fewer were killed by their presence than would have been the case if they had never been there. A least one of the judges is clearly determined to find them guilty while a second seems far more sympathetic. It's left to Richard Woolsey, who has now joined them, to plead the rest of their case. A lawyer by profession, Richard clearly knows how the game is played and focuses on that third judge.

An alien mind takes up residence in Jennifer's body and seems as confused as her colleagues are by her erratic behavior. Which begs the question; where is Jennifer?

A hive ship turbo-charged with a ZPM has received the Wraith's message from a alternate universe containing the location of Earth. The ship is now heading for Earth.

With everyone having a Sunday off - something recommended by psychologist Dr. Heightmeyer - all of the members of the Atlantis team pursue leisure activities. Rodney McKay and Carson Beckett are scheduled to go fishing; Sheppard decides to teach Ronon Dex about golf; Teyla spends some time in the gym; and Elizabeth Weir has a lunch date with the handsome Mike Branton. Their day off however is interrupted by a powerful explosion near the mess hall killing and injuring several members of the team. McKay thinks he knows the cause of the problem - a device found by two junior members of his team may have turned some of them into walking time bombs by creating explosive tumors in them.

Slowly, everyone on Atlantis comes to terms with the sudden re-appearance of Dr. Carson Beckett who, he claims, has been Michael's prisoner for some two years. He tells them what he was doing in Michael's laboratory and they set off to find the kidnapped Teyla. Dr. Keller figures out just how he's come to there at all. Sheppard meanwhile has been using all of his contacts to try and locate Teyla but they come across someone from the past. Teyla in turn has found some of the Athosians alive but they are few in number as a result of Michael's experiments. Michael explains to her just what it is he wants from her as well as his own plans for the future.

The Atlantis team endeavors to thwart Wraith plans to either find a cure for the Hoffan drug (which makes humans deadly to Wraith feeding on them) or exterminate all those infected.

Sheppard and Beckett battle zombie-like, Wraith-engineered mutants with a team of the best and brightest female SG members.

Dr. Carson Beckett is removed from stasis because he's the only one who can find the antidote to a mysterious virus that has incapacitated base personnel, beginning with Dr. Jennifer Keller.

Sheppard and the others are now in control of the one remaining hive ship with most of the Wraith transformed into human form, courtesy of the retrovirus. They do learn something interesting about female Wraiths, however. After they return to Atlantis, the question becomes one of what to do with the Wraiths who are again human, especially Michael who has proved to be quite helpful. Elizabeth Weir meanwhile is surprised to hear that she is to return to Atlantis as the expedition leader. She will be accompanied however by Richard Woolsey who is to review her leadership and make recommendations to the International Oversight Advisory on whether she should be allowed to continue.

While Teyla and Ronon investigate the mysterious death of Major Lorne, the Genii Ladon Radim contacts Atlantis. He wants to trade a ZPM for weapons supplies.

A plague of sorts is spreading across the Pegasus galaxy and Dr. Keller estimates that hundreds of thousands will die if they don't don't find a way to stop it. Her research shows however that the disease's origin is with the Hoff, who had been working on a way to kill the Wraith. Sheppard and the others think they know who might be spreading the virus and why. Teyla meanwhile believes she is receiving messages from Kanaan, the father of her child. She's getting his messages while sleeping and most think she's just dreaming. She follows the clues he gives her but she is taken prisoner by an old enemy who has very specific plans for her. In their search for Teyla however, Sheppard and McKay find someone completely unexpected.

The team find a hidden Wraith girl, cared for by a man with a serum that he claims can satisfy her hunger. Beckett wants to perfect a retrovirus that can turn Wraith into humans.

Sheppard is infected with the Wraith retrovirus and slowly turns into an Iratus bug. To provide a treatment, stem cells must be retrieved from one of their eggs.