A disinterested Young is in his quarters when Camille calls to tell him he's late. He goes to the meeting, where Camille is explaining that Homeworld Security wants Ginn on Earth via the communication to tell them what she knows about an upcoming Alliance raid. Young doesn't pay attention and finally gives his assent after Scott gets his attention. Camille goes to see Ginn, who is slow to open her door. She claims that she was sleeping, but Camille notices Eli's shirt on the bed.
drops out of FTL for no reason again, and there's no sign of Rush. They detect a ship ahead and watch as they draw closer. It's an alien ship of unknown design, and appears to have taken major damage in battle.
On the hidden bridge, Rush activates the retro rockets and guides the ship closer. They send across a kino and determine that it's deserted. Rush shows up at the control interface room and ducks Young's questions about where he was. He wants to send over a boarding party, and Park suggests they jump across in jump suits. Rush volunteers to go, insisting he's the expert on alien technology, and Young goes with him. Scott figures that he should go, but Young says that he'll keep an eye on Rush.
Eli goes to see the quarantined Chloe, who knows he's been working with Ginn. Eli apologizes for not seeing her, and Chloe is glad that he's happy with someone.
Young and Rush have a kino tow them to the ship and they board through a gap in the hull. There's no life support, and search the halls for an engineering panel. They find pods like the ones they encountered on the seed ship, but Rush is sure the kino would have noticed any aliens. Rush finds an engineering panel and seals off the hull breaches, and then activates life support. As power is restored, the derelict's engines activate. The power runs out after a few seconds, but the derelict is now on a course away from Destiny
and the engineering panel can't provide access to navigation or propulsion.
Eli and the others try to figure out what to do, but they have no options if they’re unable to control Destiny
. Young then turns to Rush, who reluctantly admits that he's created a program to take control of Destiny
's maneuvering jets. However, he warns that they need an expert, and suggest Dr. Amanda Perry. Young tells them to get Amanda on board via the communication stones.
Simeon comes to see Ginn and accuses her of potentially betraying herself to Eli. Camille arrives to collect Ginn, and tells Simeon that it's none of his business. Eli is waiting for her and Ginn assures her that she knows what she's doing. She'll be providing her body for Amanda. Camille warns that she'll have to stay on Earth until Amanda has fixed their problem. Amanda arrives in Ginn's body and assures them that she's been fully briefed.
Rush coordinates with Brody and the others. He then suggests that Young investigate a section of the ship that might have shuttles or escape pods. Meanwhile, Eli brings Amanda to the control interface room, and Rush sends him to the engineering room to help Park. After Eli leaves, Rush shows her a series of algorithms and she starts solving them.
Young calls to tell Rush that there's no sign of a shuttle, and that he'll continue exploring.
Amanda solves the algorithms and realizes what they indicate. She brings up the ship's plans and calls Rush, and he indicates that she has to go to the bridge. As Amanda leaves, claiming she's going to Eli's lab, she encounters Simeon. She explains that Ginn is on Earth, and Greer arrives before Simeon can interfere further.
Following Rush's concealed directions, Amanda goes to the bridge and activates it, putting it in ready position above the ship's hull. She then calls Rush, who establishes contact on a discrete channel. He says that it's time for them to get to work and explains that he's broken the ship's master code. Rush needs her because he doesn't trust anyone else, and Amanda agrees to help.
Eli gets to the control interface room and has no idea where Ginn is. He calls her over the radio, but Rush tells her not to answer. Destiny
then turns toward the alien ship as Amanda takes control. Rush says that things have changed since she was last aboard the ship. Amanda finally calls Eli and says she fired the boosters to guide them back toward the derelict. Eli doesn't believe her, and checks her work on the recorded video feed. He solves the equations himself.
Amanda assures Rush that they'll be there within the hour. Young arrives and secretly listens to their conversation.
Eli, Brody, and Volker follow the directions in the algorithms and find the bridge, Eli angrily demands to know what's going on, and how long Rush has had control of the ship. Aboard the derelict, Rush realizes that Young is there. He tries to explain, claiming that he was waiting until the time was right to reveal the information. Young attacks him and beats him bloody, and then demands to know if that was Rush's entire plan. Rush insists he had no choice because he couldn't trust Young, and there are others who feel the same. He warns Young that no one will follow him, and that he's too apathetic to make command decisions.
Rush explains that the code unlocked huge amounts of information, and that someone could have used it improperly. Young points out that Rush handled it improperly and got Riley killed, and Rush concedes the point. The colonel asks about the simulation, and Rush explains that it was the ship controlling it until the end until he put the ship into FTL, making it appear that the ship had decided that Young was a suitable commander. He asks Young to assess himself, and notes that Young may have been but no longer is up for command.
Amanda explains that she thought Rush had a good reason to keep the bridge a secret. Eli wonders if Rush will still be alive when they get there.
Young tells Rush that he couldn't have hoped to keep the game going forever. Rush explains that the ship has a mission, and that he's learned that Destiny
's mission is to locate an artificial structure buried within the background radiation of the Big Bang, a potential sign of intelligence. They can't see the structure with their technology, and the Ancients launched Destiny
to search for clues. Rush broke the code and accessed the archive, and they can use the Ancients' data to find the structure. He insists that they have to see the mission through, and tells Young to embrace the mission. Rush suggests that if they can find the structure, they can gain control of space/time and change things, controlling their fate. He asks Young to cooperate, and promises that he won't keep any more secrets. Young laughs at him in disbelief.
arrives and Rush tells Amanda to circle back and line up the airlocks. As the two men get into their suits, Amanda guides the ship in. She grazes the derelict and flies by, and then matches its speed. However, they have no way to get Young and Rush back, and the derelict is spinning. Young and Rush tell the others that one kino is damaged and the other one is lost, so Eli suggests that they use the derelict's centrifugal force to propel them back. Brody and Volker warn that the calculations are insurmountable, but Eli insists he can do it.
The two men get out onto the hull through the breach. Eli has Rush jump at the exact moment necessary and he flies across space, landing safely on Destiny
's hull. Young goes next, but releases too early and hits the hull at the wrong angle. As he bounces off into space, Rush grabs him and pulls him to safety.
reenters FTL while Eli masters the controls. He confirms that the database shows several planets up ahead, and brings them out of FTL.
In his quarters, Simeon looks out the porthole and considers the nearby planets.
Rush goes to see Amanda in Ginn's quarters. He carries alcohol, and they share a drink together. Rush admits that the crew is angry at him, but the truth is out and that's a good thing. He admits that he still doesn't trust Young, but he has no choice. Rush then apologizes to Amanda for putting him in an awkward position, but she's flattered that he chose to confide in him. He admits that she's the finest person he knows, and says that he's thought a lot about seeing her again. Amanda says that she's done the same. They start to kiss, but Eli comes in. He tells Rush that Young wants him on the bridge. Once Rush leaves, Eli warns Amanda that sometimes people using the stones forget that they're in someone else's body.
As Eli leaves, Simeon emerges from the shadows and enters Ginn's quarters, confronting Amanda in Ginn's body.