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.

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.

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

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.

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.

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.

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.

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

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.

While exploring a new planet, Sheppard started to watch a strange crystal. He doesn't know why, but he had to touch it. Back on Atlantis, everybody but him started to have some bad nightmares.

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.

Having been told by the Genii spy on New Athos that her people were still alive, Teyla asks permission to visit a man named Davos who is a legendary seer and may be able to help her. When they arrive, Dr. Keller realizes that the man is dying. His ability to see the future is real, but the snippets of the future he is able to show them are open to interpretation. John is called back to Atlantis when they receive a message from the Wraith whose life he had previously saved. He offers to work with McKay to fix the nano virus that is now malfunctioning. As if this weren't enough happening, Richard Woolsey arrives from Earth to undertake Samantha Carter's 3 month evaluation.

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.

Radek discovers an alien device that Rodney finds holds serious surprises. Sheppard runs into a reincarnated Acastus Kolya who plans to attack Atlantis. An IOC representative arrives to replace Woolsey who receives advice from a mysterious woman.

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.