Manga Space: A boy gets uploaded as the AI to a space battleship

 

Unparalleled Path- Reincarnated as the AI for a Space Battleship is about a Japanese school Student who is (spoilers) hit by a truck on his way to school.

When he regains conciousness, it is ten thousand years in the future and he is now the AI for a Space Battleship called Capricorn.

This is not so much an Isekai where the student gets reincarnated into a fantasy or trapped in an online space game. Rather it looks like he was donated to scientific research on his death and they uploaded his brain.

It has the ethical dilemma of erasing an uploaded conciousness that is from a sentient life and not just a computer developed AI. 

There is a fascinating story developing here and its worth your time getting to know it.