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.

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

Rodney investigates a ZPM from a planet whose inhabitants kill themselves when they turned 25 years old to prevent the Wraith from feeding on them.

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.

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.

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

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.

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.

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

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

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

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.

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.

With a damaged ZPM, and diminished hopes of survival, the Atlantis team finds themselves stranded in the middle of empty space with hardly any time before they run out of power completely. Dr. McKay is challenged to the max as he tries to find a way to save Atlantis from its doom. Meanwhile, Dr. Keller races to treat Weir's increasing head injuries, but the only answer she can come up with could have grave results for everyone on board.

Rodney McKay awakens in his lab, tied to a chair and with no memory of who or where he is. He did seemingly leave himself a video message telling him to look for Teyla. The problem began some 14 hours before when Dr. Katie Brown returned to Atlantis with plants from a planet she had visited. The plants had been cleared through the normal quarantine procedure but she is soon afflicted with severe headaches and loss of memory, eventually falling into a coma. Memory loss begins to afflict other members of the crew but they soon become distrustful of one another, making conclusions based on false assumptions and a misreading of the situation. Fortunately, there are two members of the team who seem to be immune.

A transmission from space leads the team to the discovery of a breeding ground for Wraith soldiers.

The IOA is conducting interviews back on Earth to ensure that any personnel serving on Atlantis (in particular, aliens) are suitable for their roles. The episode opens up with a pregnant Teyla having been interviewed and reporting back to Atlantis. Ronon is next. Col. Carter is unsure about Ronon's ability to handle the IOA's interview and therefore asks Teal'c to come to Atlantis in a coaching capacity for Ronon. After a rocky start to their relationship, Ronon and Teal'c return to Earth, via the series of Stargates and a Midway Station, that McKay had previously designed. The Midway Station between the Milky Way and Pegasus galaxies serves primarily as a place for those traveling between the galaxies to serve a 24 hour quarantine. While Teal'c and Ronon are serving their quarantine in the extremely cramped Midway Station, it is boarded by the Wraith, via the Stargate, with the intention to travel to Stargate Command on Earth. They achieve this objective, but only with Teal'c and Ronon in tow. What ensues is a battle between the Wraith and the duo of Teal'c and Ronon, for control of Stargate Command.

Teyla risks her life on a daring mission aboard a wraith hive ship.

Jennifer, Ronon and Rodney find themselves in the middle of a Wraith hunt when Jennifer is kidnapped by a runner, Kiryk, to help him with a humanitarian mission.

Dr. Daniel Jackson comes to Atlantis in search of a lost Atlantian room. The discovery reveals a new race. Daniel and McKay are kidnapped by the new race and are forced to finish a device which may kill the Wraith. Todd feels betrayed and takes the Daedalus.

When the power is shut down and most of the inhabitants are locked out of key controls, it is apparent that Atlantis has been taken over by an off-world group, soon identified as Michael and his hybrids. He is after Teyla's newborn child who is key in his quest to gain control of the Pegasus galaxy. While Sheppard and McKay try to get their hands on a jumper to launch an attack, Ronon and others who were taken prisoner by Michael during his initial invasion launch reprisals of their own. When Teyla manages to get away and hide, Michael gives her a simple choice: surrender herself and her child to him or he will use the city's self-destruct mechanism to kill everyone.