Dr. McKay and Dr. Zelenka have determined that the Wraith hive ships will pass by the satellite weapons platform (seen first in "The Defiant One") in about 49 hours. Dr. Weir sends McKay, Dr. Grodin and Lt. Miller (as their pilot) to try and reactivate it and use it against the Wraith ships if possible. McKay says one Naquadah generator should power the weapon enough to destroy all three Wraith ships headed their way.
Weir also sends teams out to find a new Alpha Site, as the old site's location was discovered by the Wraith. A new Alpha Site will be needed because the Wraith only want to take Atlantis to get the location of Earth (as determined in "The Gift"). Therefore, if the Wraith can't be stopped, Atlantis will have to be destroyed and SGA crew will have to evacuate to an off-world site. Sgt. Bates says Teyla shouldn't be allowed to go on these missions, as he thinks she gave away the location of the first Alpha Site to the Wraith. As they leave the meeting, Teyla takes offense at Bates' comments and knocks him to the ground with a vicious blow to the head, and more words are exchanged.
Zelenka, while working on the plan to destroy Atlantis, determines the destruction won't likely prevent the Wraith from retrieving the location of Earth from one of the many Ancients' data cores. This is because the Ancients built in a lot of memory redundancy into their data cores. Zelenka suggest they use a worm to erase all the data in all of Atlantis' data cores, and Weir agrees.
Later, Bates is found badly beaten and unconscious. Teyla is suspected, until Dr. Beckett finds it was a Wraith that had beaten Bates. They theorize it is the Wraith from the scout Dart ship (seen in "The Brotherhood") that blew up over Atlantis. Teyla says the Wraith could have used the beam technology to beam himself into the city before the ship self-destructed. They are able to locate the Wraith using their internal sensors and capture him. After naming him "Bob," Sheppard and Teyla interrogate him to find out what he had been doing to Atlantis' systems for the last month or so. To get Bob to talk, first Teyla tries a telepathic connection, which fails, and then Sheppard shoots Bob with his pistol for answers without success, until Bob is finally dead.
Meanwhile, McKay and his team reach the weapons platform in the Puddle Jumper, and after some work, succeed in powering it up. However, an EVA excursion for a final repair is needed to get it ready to fire. In the process of making this repair, they find they can't retrieve Grodin. The repair has blocked the circuits for the access door needed to get to the Puddle Jumper. Grodin decides it's best if he stays behind to power up and fire the weapon at the right time. He succeeds and the weapon is able to destroy one Wraith ship before it breaks down. [Spoiler at this point]
The two remaining Wraith hive ships continue on to Atlantis to retrieve the location of Earth and its galaxy. The Atlantis crew does not know if their elaborate plans to erase the memory cores and destroy the city have been thwarted by Bob's activities, or not.
To be continued...