I'm not getting into a grand argument with you over my little pet idea, since I'm not particularly concerned if it's true or not, but I'll at least explain my thinking.
All of it completely hinges on Nero randomly carting off with Sonon's remains, so this isn't really a very founded theory, I just thought it'd be a fun way to connect the Yuffie stuff in. Keep in mind that I'm imagining a sort of minorly rebooted version of Dirge's online mode story, not exactly the same, so stuff like
Nevermind the fact the playable Tsviet can be a woman
doesn't matter. Sonon would just be filling the role that the nebulous non-person player character filled before.
the recruit is a entirely new member of Deepground who's recruited by Restrictors and implanted with the restriction chip that's connected to the Deepground supercomputer Patricia.
We'd kind of be retconning this part a bit. In my reimagined version of the scenario, Sonon would have his memories rewritten by Shelke to believe he's an ex-SOLDIER now Deepground member. Using deception, they'd slip him in among the new recruits.
That chip is implanted by Shinra to ensure the DG SOLDIERs obey Restrictor and can be physically restrained and killed if they disobey. Why would Nero implant that in Sonon?
He'd still need the chip in order to blend in. I'm assuming they'd have a way of checking. I know the Tsviet's plan hinged on a defective chip, but we never see how they know the player character has one before they start manipulating them, so maybe they had a way of influencing that too.
Why would Shinra let Nero "recruit" anybody since he's a simply fighting tool who's so dangerous they have to keep him locked up due to his volatility? They'd just let him do what he wants with a potential candidate?
No, they'd sneak him in, Shinra wouldn't know. I'm kind of imagining this as a spur of the moment idea Nero would have, having seen Sonon go toe-to-toe with himself, a top ranking Tsviet, and thinking he might be of use in Weiss' plan to overthrow the restrictor. He'd keep him stored in his darkness and somehow slip him into the new recruits later.
If the Tsviets could just do that with Sonon themselves why would there need to be an elaborate scheme to trick the player character, make them think they had a sibling, and overcome the chip?
You see, the sibling thing is another part of the minor retcon. Rather than making the player character believe they have a sibling at all, they instead overwrite the memory of Melphi's death with what they want him to believe, ultimately imposing the restrictor over Scarlet's role in her death. His backstory about tragic little sister death is what spawned this idea in my head to start with, it fell neatly into place.
And before you respond, just keep in mind this is just some fanfic head canon I made up for fun.
Sonon literally died. His death scene is called "Sonon's Last Moments."
This could still be true. It probably IS. I just think it's a fun idea.