Five wants The Android to help her process the recording of Two and Three plotting someone's demise but finds her unconscious after being zapped by the mystery assailant. Two and Five discover that The Android's neural chip has been removed ... and that she has a Volkov-Rusi patch in her hand. Two figures a Volkov-Rusi operative must still be on board!
Two gives Five a gun (because she's a grown-up now) and divides the gang into pairs to find the intruder who deactivated The Android. Two goes with Three and asks why he gave up the vault code to Wexler and the hijackers. He says that it was the logical call: they need her to run the ship. Romantic tensions hover in the air.
Elsewhere, Four tells One that once he lands and gathers his resources, he will take back his throne, and it bothers Six that Five has become so adept with a gun. He says that all along, she's tried to be like them, but they've wanted to be like her. They failed, as they couldn't escape their criminal past. She tells him that he's wrong, as they've become a family.
If there's an intruder, he or she is nowhere to be found. Five reminds them that they should check the vents, which comes up with nada as well. They go into the weapons room and discover the shock stick is missing; as only the Raza crew has the code to the room, they deduce that one of them incapacitated The Android. But who?
The crew suspects that whoever disabled The Android wants to "finish what they started" when they erased their memories. Six wants everybody to stay together but Four won't hear of it and leaves to train in solitude. Three tells Two that they should kick One off the ship because One got on board illegally and is probably the villain. Two says she knows One's whole story and doesn't believe he's guilty, though Three wonders if she can really be trusted to lead because of her relationship with One.
Meanwhile, One tries to convince Four that they need to isolate Three. He reveals his own backstory but says that, while he originally assumed he came on the ship to get revenge on Three, he doesn't think so anymore: he had a chance to kill him, and didn't. Either way, Four won't commit.
Finally, Five tells Six that she suspects Two, and that he better be careful because she'll likely come after him or Four next.
Two calls everybody into the mess for a meeting and brings a pitcher of water. As they argue about what to do, One rejects Two's offer of water, and Four is the only one who drinks ... after which he goes into a seizure and passes out! Two suspects that the entire water supply is laced with powerful barbiturates, which makes Three and One hurl accusations at each other. Finally, Two declares a search of everyone’s quarters for the missing shock stick, though it's nowhere to be found.
Five asks Six to stay in her room, where she plays him the recording incriminating Two. Afterwards, they find a corrupted file on Five's computer made the day they went into stasis. Six thinks Five designed the program that wiped out their memories, but that she didn't intend for it to do that; he figures she did it to help someone, not hurt him or her.
Six leaves Five's room to investigate a noise, and when Five follows shortly after, she finds him unconscious. Someone injected the now-comatose Six with the same poison that Four drank. As the crew begins to bicker about who did it, the ship lurches. Two, Three and Five rush to the bridge and find that the engines are down ... and One is suddenly missing. Two and Three go after him and lock Five in the bridge "to protect her." Hmm.
One finds Three and points a gun to his head, and they argue over which one of them is the villain. Two sneaks up behind One and knocks him out with her gun. They lock him in his room, where he wakes up, claiming that he's innocent.
Suddenly, The Android's clone appears to Five and tells her that The Android's emotions prove that she's defective. Five orders her to delete herself, which she does, and then goes about looking for a way to free herself from the bridge and One from his room.
After Two turns on another engine to get the ship moving, she and Three find that Five has indeed escaped; and worse, a Galactic Authority ship is coming right for them! Oy.
FTL is still down, so the Raza can’t bolt from the authorities. All they can do is stand and fight, but as somebody’s locked down all of their weapons, that's not really an option, either. Three confronts a gun-toting One and insists that he hand over the password to unlock the weapons, though One claims he doesn’t know it. Two appears behind One and tells him to drop his weapon. One refuses, saying that he won't be tortured for information he doesn't have. Then Five shows up pointing a gun at Two, saying she won’t let Two hurt anyone else. Five believes Two played One and Three against each other so that nobody would suspect her.
These people need family counseling.
As the Galactic Authority prepares to board the Raza, Two says they have a few minutes to unlock the weapons, get to the ship's entrance and fight the invaders ... but they need to trust each other. At that moment, the doors around them close and poison gas fills the room, knocking them out cold.
Season One ends with Galactic Authority troopers carrying each unconscious crew member of the Raza down the hall. At the end of this sad parade, walking next to a member of the GA, is … SIX!