This contains spoilers!
Thank you for the feedback, it helped me a lot in how I should write my stories moving forward. Now for some of your confusion with the end, I don't know if I conveyed it well enough, but the reason why John comes back was because the AI made a mistake when making another clone of john and the AI didn't reset his memories. Another thing that I think will help with some of your confusion is the mind of the AI is broken and which causes it to be insane and evil. one more thing I saw you talk about in your response is the story takes place in a space ship heading to the planet that John walks out on, I just wanted to clear that part up.
And again, thank you a lot for the feed back, this was the first time I wrote something like this, so I appreciate the good criticism.