With Destiny nearing the edge of a galaxy, Young adjusts to the notion Eli, Chloe and Scott are lost. Meanwhile, Rush tells him that Destiny is losing power and won't make it to the next galaxy. Brody suggests increasing the engine's efficiency, but since they have no idea how the engines work, Rush advises bringing the consciousness of Amanda Perry, an expert in Ancient engines, onboard. Amanda, however, has severe physical disabilities, and Young warns any potential volunteers that switching consciousnesses will be a big adjustment. Lt. James is the first to volunteer, but panics and returns to the ship. Camille stoically takes her place, and the reunion between Amanda and Rush is tender. James, back on the ship, has a mysterious experience, which she dismisses.
On Earth, Camille and her wife struggle with the limitations of Amanda's disability, and Camille's consciousness and Amanda's are briefly switched - there's been an explosion on the ship, and Camille knows that something is seriously wrong. James heads to the sick bay and tells TJ about her episode, describing it as a sort of out-of-body experience. Franklin is carried in, badly shaken, and he and James share a moment of non-verbal understanding.
Amanda's tour of the ship's systems is cut short as the team try to solve the mystery of the explosion. While they're viewing the damage with kinos, the ship alerts them to an incoming wormhole, and they prepare a defense team, but are surprised by the miraculous entrance of Eli, Chloe and Scott. As they work together, Eli learns that Amanda had feelings for Rush. They discover that the explosion eliminated a damaged module in the FTL drive that was sapping energy, and attempt to bypass it. Eli suggests using the robot they found in the cargo bay, and Amanda programs it to perform repairs. With the clock ticking, Young tells Rush that, if it comes to it, he'll sit in the chair to save the crew.
Young sends a recon team to the planet from which Eli's team just came, and the kino delivers the disturbing footage of alien ships exploring the recently deserted camp. Living on that planet is now no longer an option - they must fix the ship, or die. It takes weeks, but finally the robot removes the damaged drive. With this small victory Rush and Amanda go to Brody's still to unwind. Under the influence of Brody's rotgut, Amanda expresses her feelings for Rush, and though he reciprocates, the memory of his wife's loss is still too painful for him to move on. As they share this moment of intimacy, TJ alerts them to an emergency in the control room.
James confesses that she thinks she caused the damage to the ship by neglecting to wipe her imprint off the communication stone. An alien may have been able to use this to access Destiny. As the crew swing into military defense in anticipation of imminent alien attack, Franklin breaks his vegetative state to utter, "the chair." Alien ships appear on the horizon as James urges Young to let Franklin sit in the chair. Once enthroned, Franklin orders Young and Rush to leave the room. The ship jumps, and with the ship and crew safe, Amanda goes home. Rush and Young go to retrieve Franklin, but discover the chair room completely empty.