Ooh, I like this one. I'm not sure where to start, but I'm thinking that >!we're going to "ethically" clone the passengers, aging them extremely fast for cellular growth, and use the new bodies and their sturdier tissues as material for ship parts. The AI may be oblivious enough that the passengers wait up to see flesh, skin, beating muscles, and faces adorning the walls. After ensuring the structural integrity of the ship, the AI will use the softer tissues and organs as fertilizer to regrow the crops that were meant to feed the passengers. I guess that's not really important, but the main point is the shock value of the passengers waking up to a ship made of human body parts!<.

Plan out the entire story in advance, and make sure you spread hints (or implications) of the major reveals throughout the story, because the worst thing is if the reader feels like the ending or the twist is half-assed. You need minor reveals as well; you should be revealing impactful information like a slow drip--each individual piece of info could be a crumb about the world, the characters, or the events that transpired, but the important thing is to give small crumbs over time so that it doesn't feel jarring. You want a story that is well-contained, flows well from the beginning to the end, but also completely flips the perspective that the reader started with in the beginning by the time the reader gets to the end.