Have you tried The Hero Project: Open Season? You can continue off of your old character, and even talk to Prodigal as a Mechip. Not finished yet, but I think you might be able to find her/ resurrect her.
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This is a rather characterful and amusing fanfic I came across, with Prodigal alive and well.
https://archiveofourown.org/works/7676608
On the subject of Prodigal (whom I played a law abiding hero to romance, because he thought he could change her, but then his own lawful score took a hit when he punched out Victon at the end), I can’t help picturing her these days as Pitohui, the villain from the recently finished ‘Gun Gale Online’ SAO spinoff anime.
Black bodysuit, huge arsenal of exotic weapons, crazyface, hops about laughing and killing people. The only difference is that Prodigal had a terrible childhood, so we love her, while Pitohui is suicidally depressed despite her huge fame and wealth, consoling herself by beating up her boyfriend and threatening to kill him…so not so much love there.
It’s the name of the three people you saw in the Meek headquarters that is actually three infini individuals including yourself
I thinl they know by now, given this thread is 4 years old 
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Does anyone know how to scan prodigal DNA to get the sample MeChip?
You should jump into The Hero Project series, you will find her there again… I mean for how I remember (it was years ago I played) Prodigal died but kinda cheated death so you will meet her again. With the other character in the Hero project (is a total different character )
The good about the Hero project series is that it use the saves from the Hero rise series to determine the 1st Hero so you will have both your characters meet each other in the story at some point. I thinked by how the Hero project series ended that it wanted to re-connect to the VERSUS series (BUT…with “Versus: deathscapes” it kinda become a let-down so don’t go read VERSUS that for me is a dead horse by this point). In any case to answer the question. Yeah there is hope for Prodigal
I think they might be wondering how todo the scan in HR3? Wasn’t that automatic, though?
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Aye this is what I meant. The option was greyed out for me