Meh, I will just bag my idea, but I have another idea.
Going with the "Dark Factory" idea, I am thinking that what if the heroes were heavily damaged by their dark counterparts? I have decided that after the heores have been heavily wounded, they have been exposed to some type of substance called GN Particles (That was from Gundam 00, but I am a fan of Gundam and I wanted to use that). They are turned into beings that look like the Virtuaroids (That concept came from Virtual-On; which I also have a interest in. The Heroes actually look like the VRs from Oratorio Tangram) and now, they are ready to fight their counterparts with their new powers and weapons.
Off topic: if some of you don't know what Virtual-On is, then this is what it is:
