"The stuff my gene works on," John adds, "Like the little scanner." Then he turns to squint at TJ. "Guess it must have been a pretty special ship if the Lucian Alliance went to all that trouble. Did you have a carrier with you? To get it working, I mean. Or someone who had been given the gene therapy?"

Since presumably on an Ancient ship you'd... need someone with the gene to be able to get into the systems and take control? Unless it was, weirdly, all activated already? John has been on mostly-abandoned ancient ships before, even if they were nothing like Destiny he's still picturing it like that. Like the Aurora or something. Brightly lit, with cryo-chambers maybe. If they'd been dialled into some bigger version of that with it's own gate then... well, presumably they'd be aiming to take control and grind it to a halt so they could re-synchronise the gate and dial back, right? Or at least turn it around and begin making jumps to somewhere they could dial back from.