A question:
Will you be able to control the dark one's abilities, or will they occur during the story?
I'm planning on making it with RPG Maker, and the Dark One's will have combat based abilities that you can control in the fights. Also, in my mind, the weapons they use are manifestations of dark energy that they make themselves, so that also is a usage of their power (I haven't quite worked out the weapon obtaining system though, and will nail that down more thoroughly once bootcamp and the best rpgmaker download I can get my hands on ae up and running)
The Dark One you play as will also have travel based abilties. The ability to hop between universes requires the creation of a dark matter portal, but this will probably just be a glorified teleport system. I imagine the time travel will work much the same way, with each "world" you can teleport to having 2-3 timezones you can hop between (and hopefully I'll be able to make the map sets mach each timeframe) but again, this will probably just look like a glorified teleportation/warp thing.
Mainframe access will solely function as part of the story however.
Also, I've made the decision to move forward with The Dark Ones as the my project, and again, once I have everything up and running, I'll probably start a devblog and all that fare.