If this mod ever gets its own story, perhaps it could be that VR is being hacked by a master group of hackers, altering the VR training mode into a roguelite dungeon crawling.

However you're not the only one that can alter the VR training mode's code. A coder on your side can help linearize the system and make it salvagable, dropping upgrades and diskettes to make you stronger as you progress through the altered VR world, with failed attempts sending you back to reality to spend the XP, or in this context, codelines, to add permanent upgrades in future attempts.