The ship has several thousand automated systems, each with its own control hardware.
The last two weeks of diagnostics indicate that these systems are clean. We found no booby-traps, and the only back-doors are the manual overrides.
All we need to do is install a fresh A.I. core, and the ship will be fully operational.
You make it sound easy.
It's only a little bit more complex than a brain transplant, and without all the pesky protesters.