The Wraith are now only about two days away from Atlantis. Thanks to Teyla's psychic connection to the invaders, she has seen that the Wraith armada will soon pass by the only surviving Lagrangian Point defense satellite (located 15 minutes' jumper flight from Atlantis), which Drs. McKay and Zelenka now think they can make operational with just one Naquadah generator. McKay, Grodin and Miller fly there by puddle jumper and race to get the satellite online in time to fend off the Wraith armada.
Meanwhile, Maj. Sheppard and his team, including Teyla, go scouting for a new Alpha site, because the original one has been compromised. Weir and Zelenka devise a plan to completely destroy Atlantis so that no usable piece will remain for the Wraith to exploit. Zelenka is more concerned about the Ancient database's remarkable ability to back up data. If the Wraith recover even a tiny portion of the database, they will be able to recover all of it. Zelenka develops a computer virus that will tie in to the self-destruct countdown and wipe out the database. Unfortunately, even with McKay's new data-compression technology, they can download only eight to nine percent of the massive database to take with them to the new Alpha site.
Unscheduled offworld activation: Sheppard and his team come in hot from the new Alpha site. Immediately, Sgt. Bates berates Teyla for having psychically betrayed the new site to the Wraith. But Bates' rebuke is misguided: Sheppard, Teyla and Lt. Ford were being chased by a Tyrannosaurus Rex, not a Wraith. The tension between Bates and Teyla reaches a fever pitch. Consequently, when Bates is later found unconscious with broken bones and scratches, Teyla is suspected.
Meanwhile, McKay hooks up the Naquadah generator to the Lagrangian Point satellite and restores its life-support systems. The generator pumps out enough power, none of which is reaching the weapon. The energy is being stored in a buffer. The main power conduit is damaged. The power must be rerouted around the damaged circuits, which are located on the exterior of the satellite. McKay draws the short straw and goes EVA from the jumper, while Miller takes the helm. Grodin remains in the satellite control room to monitor McKay's progress.
Back at Atlantis, Dr. Beckett completes a DNA test on Bates' uniform and delivers conclusive and alarming news: There is a Wraith in Atlantis; when the Wraith dart scanned the city and then self-destructed ("The Brotherhood"), the pilot beamed out and has been reconning the city for the past two weeks. Zelenka is able to expand the biometric sensors monitoring the gateroom (from which they thought the Wraith would be more likely to invade) to the rest of the city and picks up the Wraith's signature. Sheppard, Teyla and Ford track him down, stun him and throw him in the brig.
McKay fixes the problem on the satellite, but it seems that when they rerouted power from the buffer to the weapon, they lost power to the docking control and the airlock. The jumper can't dock to pick up Grodin, and he doesn't have a space suit to EVA. The Wraith ships are very close. Grodin insists that McKay and Miller get to a safe distance first, and return for him only after the satellite destroys the Wraith ships, and he re-establishes power to the docking station and airlock.
At Atlantis, the Wraith prisoner is not talking. Sheppard repeatedly shoots him until he speaks. All he says before he dies is that the Wraith will find the Atlantians no matter where they flee, just as surely as they will find Earth.
The satellite fires and destroys one of the approaching Wraith hive ships. McKay radios the good news to Dr. Weir. But the rerouted circuit overloads, causing the satellite to explode, with Grodin onboard. A shaken McKay and Miller return to Atlantis.
Dr. Weir addresses the city over the P.A. system and orders the evacuation to begin. Zelenka puts the virus download in standby mode.
It appears Atlantis will soon be lost forever.