I checked through my beta feedback. (I've been skimming to see what changes were implemented and what wasn't.)
"I'd love to see a bonus ending. If say you've your relationship with Prodigal maxed, or as a reward for a perfect legendary score, where there's a single cryptic note which leaves a hint of hope that she's survived and that you will actually find her."
I wanted a glimmer of hope but maybe that's what fan-fiction is for, or just crazy forum theories.
For me, here's my own made-up alternative ending.
Jenny's life is saved and she becomes Null fully, so why isn't that also a possibility for Prodigal? We know that artificial intelligence exists too. There's that AI (was that Processor?) who shows up in the first game.
Prodigal, dies, saving the life of the person she loves most in the world, in an attempt to redeem herself. You go home, you mourn her loss and what might have been. Only then your Mechip goes fuzzy, and the holographic image is replaced with the one person you most want to see. "Miss me, Chicken?" Prodigal asks. "You didn't think I was really dead, did you? Always have a backup plan."
While infini-cancer may have ravaged her body, Prodigal's a master of machines and she was able to transfer her consciousness at the moment of death into the closest electronical device capable of storing such data. Of course the two of you are going to need to work on creating her a body, and now the whole world thinks that she's dead she's got a chance to start afresh, with you.