Young finishes a "trip" to Earth via the communication stones and goes to see Johansen. She tells him about the test results on Chloe and Scott. Scott's blood has gone back to normal. Young appears distracted, and Johansen says that it's safe to let Scott out of isolation. Young agrees, and then tells her that his wife Emily has filed for divorce. Johansen suggests that they talk, but Young doesn't see the point.
Camille brings Ginn to see Eli, and suggests that she help them study Ancient systems. She's intrigued by Eli's theory about creating a wormhole inside of a star, and Eli agrees to work with her.
Scott comes to see Chloe and tells her that he's back to normal. He insists that she is still normal, since she saved his life. However, Chloe shows him a patch of silvery material on her leg, and warns that it's spreading. Scott insists that it doesn't matter, and promises her that they'll find a way out of it.
Young is in his quarters drinking and contemplating his weeding ring when Brody calls from the control interface room. The colonel finally responds, and Brody tells him that they have a situation. Young goes to the room and Brody tells him that nine alien ships have dropped out of FTL and surrounded them. They're the same ships that abducted Rush and Chloe, and the aliens send a message demanding Chloe. Young figures that Chloe was gathering intelligence via the pathogen, and the aliens are there to collect. With 44 minutes until they jump, Young orders an attack on the aliens.
Rush comes to the control interface room and warns that they can't take on that many ships. When Young points out that the aliens want Destiny
, Rush warns that they'll collapse the shields using weapon fire, and could inadvertently damage the ship.
After getting the civilians to safety, Scott goes to the observation deck and watches as debris hits the glass. It shatters, pulling him out into space.
The systems overload and Young and the others look on helplessly as the ship explodes...
...and Young wakes up in his quarters. He goes to see Camille, who is going over repair plans. He abruptly tells them to get the weapons online as soon as possible. Afterward, Camille wonders what's going on, and she suggests that he is having issues that are clouding his judgment. Young insists that he's fine and walks away.
Rush goes to see Chloe and asks her to look at some of his equations. When she refuses, he reminds her that he tried to help her, and insists that his attempt to use the chair to cure her were real. Rush insists that there are advantages to her condition, including the fact that she was able to save Scott. He explains that he is on the verge of discovering Destiny
's true mission.
Ginn goes over Eli's notes and explains how he erred, but admits that she admires his work. Eli talks about how he wanted to be a veterinarian and talks about he managed to kill his pet hamster. Greer, on duty watching Ginn, quickly gets bored. Ginn takes Eli's hand briefly, and then admits that if it wasn't for the hamster, none of them would be on the ship now.
Young goes to sleep in his quarters, and gets a message from Brody in the control interface room. Young goes to the room and Brody tells him that nine alien ships have dropped out of FTL and surrounded them. They're the same ships that abducted Rush and Chloe, and the aliens send a message demanding Chloe. Young figures that Chloe was gathering intelligence via the pathogen, and the aliens are there to collect. With 44 minutes until they jump, Young realizes the weapons won't work. The aliens fire a warning shot, and send another message saying they'll destroy Destiny
. Rush arrives and suggests they divert all energy to the shields, and Young agrees.
The shields hold, and Scott seals off the observation deck. Six more ships arrive and add their firepower. Young watches, unconcerned, as Destiny
...and Young wakes up in his quarters. He goes to see Camille, who is asleep in her quarters. When she answers the door, he admits that he might be going insane. Young describes his dreams and how realistic they are compared to other dreams that he has. Camille notes that his dreams represent a no-win scenario and that he won't surrender, but Young doesn't think it's that simple. She suggests that he talk to Chloe, who says that she's better off in quarantine rather than out where the others are afraid of her.
As Eli eats, Greer asks him when he's going to make a move on Ginn. Eli doesn't believe that she's interested, but Greer says that Ginn is the only girl he's going to have a chance with. He says that he'll arrange to get called away the next time Ginn is with Eli, and slaps him on the back before going.
Young is working in his quarters when Brody calls him from the control interface room, Young goes to the room and Brody tells him that nine alien ships have dropped out of FTL and surrounded them. They're the same ships that abducted Rush and Chloe, and the aliens send a message demanding Chloe. The aliens fire a warning shot, and send another message saying they'll destroy Destiny
. Rush arrives and suggests they divert all energy to the shields, but Young says that it won't work. He goes to get Chloe and turn her over to the aliens, as six more ships drop out of FTL. Young sends her to the corridor with the hull breach and walks away, and Scott demands to know what he's done. He punches Young and Greer pulls him off, and Brody calls to warn that more alien shuttles are approaching. They realize that Chloe passed on the information she learned of how to shut down the shields. Young laughs hysterically as the crew try and fail to mount a defense. An alien confronts him...
...and Young wakes up in his quarters. He goes to the still to get some more alcohol, and Johansen is there to get some disinfectant. She notes that he isn't looking good, and then tells him that their baby is alive. Young insists that it isn't possible, and Johansen warns him that he's going to the same place she almost went. The colonel says that he's sorry but it's not possible, and walks away.
As Eli and Ginn work, he discovers that the computer is running a memory-intensive program. Ginn notices some photos and Eli explains that he's putting together a movie using footage from the kino. James calls to tell Greer that they need help, and takes off. Eli goes after him, while Ginn starts playing back from some of the footage of Eli talking about his mother's visit to the ship. Down the hall, Eli admits that he's having second thoughts, and Greer isn't sure what to tell him. Eli finally braces himself and goes back, and finds Ginn looking at the footage. She apologizes, and Eli starts to go... and she kisses him.
The ship drops out of FTL, and Scott goes to see Young in his quarters. He tells the clearly drunken colonel that they've dropped out of FTL but there's no Stargate nearby. Young blearily insists that Rush will figure it out and goes back inside.
Rush is on the bridge, and has no idea why the ship dropped out of FTL. Jeremy notes that only Rush can force the ship out of FTL.
Scott goes to the control interface room and asks what's going on. Eli talks about Ginn until Scott tells him to focus, and explains that the computer was running a battle simulation. Camille realizes that Young has been experiencing the battle simulations telepathically.
Rush discovers the battle simulations as well, but doesn't know why it has to do with the ship dropping out of FTL. Jeremy tells him to look closely, and Rush realizes that the simulation is overriding normal ship functions.
Camille presents her theory to the others, and they wonder if it's Destiny
's way of warning them about the aliens. Scott goes to see Chloe and asks her if she remembers sending a signal to the aliens. He then tells Eli to prep the weapons and put all available energy into shields. Scott puts his men on alert for boarding parties, and has Camille organize the civilians. She says that there's one more thing they need to talk about, and both her and Rush insist that Scott has to take command. They believe that Destiny
is analyzing their input, and is taking its cues from Young.
Scott goes to see Young, who finally lets him in. The lieutenant warns that they have a situation and that the ship is affecting the colonel's brain waves. Young suggests it might be the ship's way of tell him to give up his command, and asks how Scott will feel when he has to drop Chloe off the ship. When Young taunts Scott about how he views the colonel as the father he didn't have, Scott shoves him and tells him that he has no choice but to serve as the commanding office. The colonel responds by telling Scott that he killed Riley and tells him to leave. Scott insists that Young needs to be in command because he's the only real leader that they have, because he hasn't stopped caring.
Once Scott leaves, Young cleans himself up and goes to the control interface room. Brody confirms that there are no signs of the aliens. Young takes command and the ship jumps into FTL.
Later, the civilians discuss the situation in the mess room. Eli admits that he's uncomfortable that the ship can read their minds. Brody suggests that they know that they have the right person in command, since the ship reacted.
On the bridge, Jeremy congratulates Rush on overriding the simulation and getting the ship back into FTL. Rush insists that the aliens were no threat and Chloe never sent a signal. Jeremy agrees, but warns that there may be another threat ahead.