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.

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.

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

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.

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.