On Earth in Washington, Richard Woolsey and Colonel Telford meet with Ambassador Ovirda of the planet Langara. They want him to use his planet's naquadria generator to power a wormhole capable of reaching Destiny, but Ovirda points out that on the two previous planets where it was attempted, the planets were destroyed. Woolsey concedes the point but explains that they have a new solution, and calls in Rodney McKay.
On Destiny, Rush plays chess with Amanda's computer projection. She insists that she is still herself, but he notes that she's busy multi-tasking through the computers. Amanda concedes the point, but wishes that she could become flesh-and-blood again, and then realizes that there is a way.
Rodney begins his presentation, but Ovirda doesn't believe that there's a point. He asks if McKay would put Earth at risk, and Telford warns that if Ovirda's people don't agree to help them, the Lucian Alliance will move in so that they can open a new wormhole to Destiny. The ambassador only agrees to consider the matter once his scientists Ovirda leaves and Telford concludes that the Lucian Alliance has already gotten to him. Telford takes Young and Rodney to meet with Colonel Young, who is on Earth via the communication stones. They've intercepted signals between the Langarans and the Alliance, and are convinced the two groups are negotiating. Young and Telford explain that they are preparing to launch a preemptive strike, and need to explain the procedure to them on Destiny.
McKay uses the communication stones to go to Destiny, but is surprised to discover he's in Brody's body when he was supposed to be in Rush's. Young checks on Rush, and Chloe explains that he's in the neural interface chair. She doesn't know what he's doing, and Young tells her to find out.
Amanda is with Rush in bed and explains that he's in a virtual immersion program via the chair. She explains that she has set it up so that he can come and go as he pleases, and they have the entire ship's matrix to be by themselves.
Young finds Greer exercising and notes that he's still recovering from surgery. Lisa tracks him down and admits that he wasn't supposed to leave, and Greer reluctantly goes back to the infirmary.
McKay meets with Eli and they argue over the conclusions. Young arrives and McKay admits that Eli is bright. He insists that the procedure to create the ninth-chevron wormhole is foolproof and Eli reluctantly agrees. Young is satisfied with Eli's conclusion and they send McKay back. The colonel returns to Earth and discuss the Langaran seizure. Young and Telford insist that they will prove that McKay's proposal is safe, and that they confirm the alliance between the Lucians and the Langarans. Woolsey objects to the idea of an invasion, and Young explains that they're going to give the Langarans a peace offering.
Johansen checks on Rush, who admits that she's not sure what's going on. Young tells her to keep an eye on Greer, and then tries to figure out what Rush is up to. He tells Eli to bring Rush out of the interface so he can talk to him later. Johansen goes to the infirmary to tend to Greer, who is suffering from an infection. He asks about Volker, and Johansen assures him that Volker is fine. She notes that she's surprised that Greer is the one who got sick, but Greer says that it's better for him to do so because he's the strong one.
Eli, Park, Chloe, and Brody examine Rush and realizes that he's uploaded his complete consciousness into Destiny's computer matrix.
Amanda shows Rush around the virtual representation of the ship and says that she prefers being with Rush to existing alone as pure consciousness. They kiss, and Rush suggests that if he can interact with the systems in the real world, they can be together more of the time. Amanda points out that it isn't possible and Rush concedes the point, and then says that he has to go back to the real world. She asks him to keep their secret for now, and Rush agrees. Amanda leads him back to the chair and explains that he has to sit in it so he can return to his own body. After a final kiss, Rush sits in the chair and it activates... but they discover that he's still in the simulation.
On Langara at the naquadria power plant, the Stargate activates and the Langaran soldiers take a defensive posture. Woolsey and a soldier come through and explains that they have gifts for Ambassador Ovirda and Chief Administrator Halpurn, artifacts carved by the Ancients. The security captain insists on inspecting them, unaware that they are communication stones. Scott switches with the man, who is shocked to find himself in someone else's body. They then take the stones to Halpurn, who examines one of the stones. He switches with Young, and Young takes command and goes to the Langarans' gateroom to meet with Telford as he arrives.
Amanda tries to figure out a way to stop the simulation, but Rush notes that it's isolated and nothing she's doing is having any effect. Rush assures her that he'll be fine on his own, and she "leaves" to inform the crew what's happening.
Eli goes out into the corridor to call for Ginn, but gets no response. He explains to Brody, Park, and Chloe that the Ancients experimented with thought transfer, and he figures that Rush and Amanda came up with a way to initiate physical contact in a virtual immersion. Eli mentioned it to Ginn, who thought that it would be dangerous and then disappeared.
Young in Halpurn's body informs the security forces that they have agreed to dial the ninth chevron address to prove the viability of the connection. When Scott orders the men to stow their weapons, one of the Langaran airmen asks him in private what's going on, and that Halpurn had earlier said that opening the wormhole would be dangerous. Scott tells him that Halpurn was bargaining and leaves.
Amanda and Rush go to the virtual bridge, and Amanda explains that Ginn's disapproval of the idea is keeping Rush from leaving, and they've fixed the problem.
Telford, McKay, and a team of soldiers arrive and McKay has everyone go to work while he hooks up the Langaran mainframe. Young tells Scott to seal down every entrance into the building, and use the Langaran soldiers as necessary.
Rush and Amanda try to send him back to the real world again, and the process succeeds. They explain that he's been "gone" for 12 hours, and Rush dismisses their concerns before staggering away to get a meal. In the messroom, Rush explains to Eli about Ginn's disapproval locking him in temporarily. When Eli asks what happened, Rush leans over and explains that the experience was personal.
McKay warns Young that it will take him at least an hour to complete the arrangements. Woolsey says it's time to undertake their secondary objective, and Young takes him to his Halpurn's office... unaware that the airman is secretly listening in on their conversation.
Woolsey goes through Halpurn's files and finds the information he needs. Meanwhile, McKay argues with the Langaran scientists until Telford interrupts him. They have the Stargate ready, and McKay says that he'll be ready in ten minutes. Telford then asks if he's interested in going through to Destiny and helping them restore it to their former glory. When McKay asks if Young is in command, Telford hints otherwise.
Amanda appears to Rush to check on him, but then fades away as the FTL shuts down. Ginn appears to Eli, who is trying to get Rush out of the chair, and explains that Rush is in danger and she shut down the FTL as a distraction. She tells Eli that Amanda is blocking their efforts to get Rush out, and there's no way to do it except from outside the system. As she fades away, she tells Eli that he's the only one who can do it.
In the simulation, the unwitting Rush asks what the problem is, and Amanda says she had to initiate a brief emergency shutdown. She kisses him and fades away, and Rush realizes that she's made physical contact with him.
Woolsey reports to Young that the Langarans have refused to negotiate with the Lucian Alliances, and that Ovirda was telling the truth. Telford insists that the knowledge changes nothing. The phone rings and Young takes the call, and confirms that Ovirda is on his way.
Rush wanders through the ship and finds Eli, and asks why he's not working to get him out of the chair. He then lowers the shields, much to Eli's astonishment. Rush then goes to the bridge and tells Amanda that he's still in the simulation, and he has to find his own way out. He's dropped the shield to overload the simulation parameters. Amanda insists that it's really happening and he'll kill everyone on the ship, but Rush says he doesn't think so. The shields overload and collapse, and Destiny begins to fall apart.
McKay tries to finish the programming, while Young suggests to Telford that they need to reconsider their plan. Telford doesn't see the point, and McKay completes the work and begins the program. While Telford orders the Langaran workers out, Woolsey suggests that they call off the plan and open the Stargate to Earth so they can get out. Langaran soldiers move in as Telford insists that they need to continue and prove that they can create a lifeline to Destiny.
Ovirda and his men arrive, and Young tells his men not to fire. The ambassador realizes that Young isn't Halpurn, and warns that if they don't stop the dialing process, his men will open fire. McKay confirms that the dialing program is working, but advises Young that things will only get worse if they continue. Young agrees and orders his people to stand down.
Eli goes to the neural interface room and explains that he knows what Ginn had in mind.
Rush wakes up back in his quarters, still in the simulation, and asks Amanda why she lied. She says that she hoped to find a way to get him out of the simulation and didn't want to alarm him. Rush realizes that it wasn't Ginn's fault, but Amanda's. She explains that she programmed in the parameters that they would love each other, because that's the only thing she wanted. He insists that he loves her anyway, but Amanda says that he can't because she's only a program. She tells him that Eli is deleting her memories and Ginn's, and there's nothing she can do to stop him. Rush swears that he loves her, but Amanda disappears.
Scott and Young are returned to their bodies, and Young explains that Ovirda has agreed to release Telford and the others in return for protection from the Lucian Alliance and removal of the Stargate. Vanessa explains that she showed the two prisoners around the ship to see who was at risk, and Young notes that it was the best decision anyone has made recently.
Rush wakes up and Johansen tells him that he's been in a coma for two days, recovering from the experience. Eli explains that he transferred Ginn's and Amanda's programming into quarantine to save Rush. Disgusted at Rush's lack of appreciation, Eli walks away, and Johansen tells Rush to take it easy given how close he came to death.