Dr. Keller, the acting chief medical officer, meets with Weir and suggests she should find someone else. Weir persuades Keller to reluctantly stay on.
McKay is doing performance evaluations, but doesn't really want to do so since he doesn't know or like any of them. Sheppard's already done with his… except he gave everyone high ratings. The Apollo arrives out of hyperspace and Colonel Ellis promptly beams in with a team to set up, and asks for a private meeting. He informs them that the Daedalus has been performing flybys of the humaniform Replicator planet and discovered that they are building a fleet of ships. Ellis informs them that in 12 hours the Apollo and the Atlantis team will launch a strike on the Replicator planet, using six nuclear missiles. Ellis beams McKay up to the Apollo as the plan goes ahead. Weir is skeptical of the plan despite Sheppard figuring the Replicator fleet will head for Earth.
Weir meets with Ellis to suggest the mission is a mistake and they should conduct negotiations. Ellis refuses, going with his mission orders. McKay and Zalenka check the nuclear missiles while figuring the mission is doomed to failure, but there's nothing they can do. Sheppard tells Weir he'll be going on the mission and notes she hasn't had nay luck calling back to Earth to get the mission stopped. She wishes him luck and he leaves.
The Apollo approaches the Replicator planet and they launch the missiles. All six missiles detonate as planned and Sheppard launches in a Puddle Jumper to monitor the planet while the Apollo departs.
Back at Atlantis, Sheppard returns to report that all of the Replicator ships were destroyed. They detect something emerge out of hyperspace and assume geosynchronous orbit above Atlantis. The Apollo investigates and determines it's a satellite with a stargate in the middle. The stargate opens and an energy beam fires through and hits the Apollo. It then fires downward toward Atlantis, cutting a fiery swathe through the water. The Apollo opens fire but the satellite is protected with a force field. Rodney determines the beam powers the force field and keeps them from dialing out, and the energy will keep the gate open so it won't shut out at the end of its 38-minute cycle. Weir has McKay try to send a signal through so she can negotiate.
They establish contact with Oberon, who has been re-replicated. He refuses to back down and tries to upload a computer virus, and they're forced to break contact. McKay warns they have 29 hours until their shield fails.
The gate doesn't shut down and Sheppard suggests to Ellis that they go back to the Replicator planet and do what they can to shut down the beam at its source. Ellis suggests Sheppard should be in command. Weir is angry that she was bypassed and suspects that the military plans to undermine her. She suggests to Teyla she may resign once the current crisis is over. McKay suggests they submerge the city which will buy them possibly a week of time to come up with other measures. The water will dissipate the energy, giving them additional time. He turns to Weir for confirmation, and she agrees to the plan.
An hour later McKay engages the submersion routine and Atlantis submerges. However, it only buys them nine hours. However, Sheppard suggests they use the recently-discovered Ancient drilling platform but they need to temporarily divert the beam by sending F-302s up to nudge an asteroid toward the satellite. Meanwhile Weir announces their plan: to use Atlantis' stardrives to lift off and leave the planet, using the extra power from the drilling platform.
Ellis offers an apology of sorts to Weir before he heads to the Apollo. Sheppard will fly Atlantis using the command chair. The fighter squadron tows the asteroid into the beam, cutting off its attack. Atlantis starts to lift off from the ocean but they don't have enough power. Weir tells them to cut off the shield to yield the extra power until they get high enough they don't need the extra boost. They do so and clear orbit, and start to reengage the shield. However, the beam fires through the small gap, grazes the control room, and Weir is thrown back by the blast. Atlantis goes into hyperspace while Keller takes command of the emergency teams.
McKay reports the damage is minimal but Atlantis emerges prematurely from hyperspace because the drive engines shut down. McKay reports they only have 24 hours until they run out of power, lose the shields, and asphyxiate. They don't have the coordinates to determine where they are to use their stargate and are lost in space. (to be continued)