I recall the plot mentioning that this ship was beyond its service life. So the AI might also be an outdated version…it reminds me of the possessed AI in System Shock.
Without altering the game's framework, the protagonist might have to deal with the malfunctioning AI, or even be used as a plaything by it. The AI might even develop sadistic tendencies as the story unfolds.
The protagonist might even be forced to reset the AI to its initial state, or even destroy it.