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.

After returning to Earth for his father's funeral, John Sheppard discovers the existence of a human form Replicator loose on the population.

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.

Combat engineers from Atlantis work against the clock to rescue four of their colleagues who are now trapped in the rubble of Michael's medical compound. With Michael en route, they quickly locate McKay and Major Lorne but Sheppard and Ronon are far deeper and their rescue is not assured. When Michael's ship arrives, they decide to try to rescue Teyla who is in labor and close to giving birth. When it's all over, Col. Carter is recalled to Earth for a performance review but Richard Woolsey has some bad news for her.

A group of beings stranded in sub-space seek help from Atlantis to return to normal space. But their outrageous claims and erratic behavior strains the trust of their benefactors and forces a painful solution.