Flashback. As Velorek continues to graft Pilot's innards to Moya's innards, Pilot stutters that he's in a lot of pain. Velorek informs him he'll have to get used to the pain because it will never completely go away. Velorek proceeds with rousing Moya, reminding Pilot that all of Moya's senses and consciousness will awaken at the same time. Also, everything she feels, Pilot will feel. Pilot promises not to cry out. "You will," Velorek predicts grimly. Moya wakes up, Pilot screams and sees all sorts of starbursts and shooty-bang-bangs. Pilot thinks there is something terribly wrong, but Velorek explains that Moya realizes Pilot is not her original pilot. He sends pain signals to Moya's control collar to force her to accept Pilot as her pilot.
Present day. Crichton's pretty jaw drops. Pilot confirms bitterly that Moya only accepted him because she was tortured into it. In frustration, Pilot grapples at his innards, ripping them from Moya. Sparks spark. Pilot displays some tubing dripping purple and black Kool-Aid, "Moya is free of me! I am no longer bonded to her."
Minor chaos as the rest of the crew tries to cope with Pilot's actions. Crichton howls, "No, no, no, no, no, this is not good, NOT GOOD!" Pilot sighs that the pain is finally gone.
Later, holding a flashlight over Moya's innards, Aeryn confirms that Pilot has been in pain all this time because Velorek couldn't take the time for the bonding to occur naturally. D'Argo berates her for not telling them this earlier, and Aeryn yells back that she didn't know it was this pilot. "Kids, save it for after school. Right now, how do we fix this thing so we stop bobbing about like three men in a tub?" Crichton demands. They don't, is the answer. Not without Pilot's help. Crichton doesn't think Pilot's in a "Leviathan for Dummies kind of mood right now." I wonder if there's a Crichton for Dummies...
Flashback. Aeryn enters Pilot's chamber and watches Velorek working on Pilot. Pilot happily natters that the DRDs are responding to his impulses now. As Aeryn observes him with an affectionate smile, Velorek has a whispered confab with a few other PKs. Pilot catches a few words and loudly asks what secret project they are talking about. Aeryn freezes, smile gone, and looks wary. Velorek tells Pilot not to worry and that the project will no longer be a threat to him or Moya ever again. Aeryn leaves.