Rodney is aboard the Daedalus en route to Earth introducing the concept of the Gate Bridge that he and Sam came up with. They arrive at the midway station and prepare the experiment although Rodney notes an odd echo in the proximity sensors.
At Atlantis, they prepare for Sheppard to fly a Puddle Jumper through the gate and begin the experiment. He arrives at the midway station and they initiate the macro, but Rodney note the sensors aren't working properly. They go ahead and Sheppard arrives at SGC on Earth, to be greeted by Jack O'Neill and General Landry. On the Daedalus, they confirm Sheppard's arrival and then Rodney detects a foreign object approaching them.
Sheppard returns to the midway station and they discuss overtaking the ship, which is traveling at sub-light speeds due to a malfunction and suffering time dilation. They come up with a plan to intercept and Rodney determines it's an Ancient warship. It slows down and the captain, Helia, sends a message requesting their assistance.
The Daedalus arrives with the Ancients and beam down, and Captain Helia asks to speak to Earth's highest authority, and then takes control of Atlantis, reclaiming it for the Ancients. Helia meets with O'Neill and Woolsey and informs her that her drive was damaged in a Wraith battle. They suggest that they have the chance to remain on Atlantis but Helia refuses. She gives them 48 hours to evacuate but Jack talks to Weir and informs her that the Ancients will let one human remain as a liaison, but they want Woolsey.
Ronon and Teyla plan on remaining behind and help Sheppard pack, while McKay, Beckett, and Zelenka discuss their plans after returning. Weir is packing when Sheppard arrives to express his dissatisfaction. Rodney briefs Helia on the base and the next day they're all leaving through the gate with Weir the last to go.
Six weeks later, Sheppard returns to SGC from his most recent off-world mission with an inexperienced team when Jack contacts them through the gate from where he's helping Woolsey on Atlantis. They report that the Replicators re heading for Atlantis but the Ancients know there's an imbedded code to prevent them from attacking their creators. Sheppard wants to go back to help but Landry doesn't allow it. Sheppard talks to McKay who is working at Area 51 and is lonely--he only gets to meet with Sheppard and Weir doesn't return his calls.
At her home, Weir is reading when Beckett visits as she hasn't been returning his messages either. He talks about how everyone is worried about her and she's not taking another position. Weir admits she's not interested and Beckett strong-arms her into coming to dinner with them.
The Replicator ship is approaching Atlantis and despite Helia's assurances, the Replicators attack. On Earth, the team's dinner is interrupted when they all get calls from NORAD to report in. Jack has sent a message warning that the Replicators have taken most of the city and Jack and Woolsey didn't make it back through the Gate.
Rodney explains that their attempts to alter the Replicators' base code may have given them a chance to rewrite their own code. The Daedalus is en route, four days away, and they need the team's advice to penetrate the shields and drop a nuke. Even with the Earth gate's iris shut, the Replicators can use the Gate-Bridge to get to the Milky Way galaxy. Sheppard wants to take a team through with Carter's anti-Replicator weaponry but Landry vetoes his suggestion.
The team meet privately and McKay reveals he has a backdoor program to gain access to the gate and get to Teyla and Ronon. They quickly come up with a plan to use the gate but they need to get by Dr. Lee, with Weir providing a distraction by expressing interest in World of Warcraft while Rodney accesses the computers. Once he succeeds, they make a hasty exit. They then take out several guards and steal a Puddle Jumper, and get through the gate.
They arrive at the midway station and Landry contacts them while McKay rewrites the macro to access the bridge. He starts to order them to return to SGC but Sheppard cuts him off and they head for Atlantis.
Ronon and Teyla are meeting with a Genii representative who wants them to work for his race. They refuse although Teyla is tempted as they both need more challenging work. Sheppard and the others arrive and ask them to help take on the Replicators. They agree and the team takes off through the gate. In Atlantis, the gate activates as the Replicator look on, unable to close it off, and the team flies through the wormhole…