Sounds like an interesting storyline. I especially like the idea of playing the henchman.. He would have the hardest job of all.. first of all, he faces the wrath of his boss and all the other henchmen if he releases the prisoners. he also risks being killed by the heroes as 'just another henchman', so he has to play a sabotage/stealth mission to sneak past guards, plant bombs and assist the heroes in the downfall of his boss whilst facilitating his own escape.. but this would take quite a lot of intelligence to work so one would have to ask, why's this guy just a henchman in the firstplace if he's so smart?

I imagine this game would be something like a Final Fantasy style (only without the annoying combat system) But like FF it would take a large team with TONNES of resources to make it happen. Just writing that story in a book would take a good writer a long time.. there are a lot of loose ends to tie up and to make it all mesh together would take an act of creativity the likes I've never seen before.

I considered a large interwoven storyline for a game I was considering called Unknown Space, the original idea had different characters taken from different universes, some where gravity was reversed so that those characters could only run on the ceilings. Others were from water worlds and they had to exist within armour plated goldfish bowls with arms and legs.. they were fighting against an emeny who used interdimensional jump technology to abduct people to use as slaves in specific environments. The universe was to be random to save on the content creation, but that in itself can be difficult to work properly. The story had holes in it, but the game play possibilities were quite nice.