Sort of similar, but for the big dark ride, I would pick Hades as our connective tissue.
I mean, most of the villains are dead, so why not just have him as the focus of the ride? We enter a temple to the god Hades, get told we're all dead, board 'boats' to cross the river styx, find out that he has united the villains in an effort to defeat their various heroes (a plot line used in the Young Hercules tv series where Hades and Jafar teamed up against Aladdin and Hercules) so that he can rule the world, the villains don't like being under Hade's thumb so they all join forces to rise up against them, during their fight, we inadvertently bump most of them into the river styx, Hades thanks us for our help and lets us go free while saying, "Hey, thanks and all that, but don't think this is it for us. Sure, I'm letting you go now for what you did for me, but eventually you'll be back."