There's Marvel Prep (marvelprepmods which is a High School based Marvel game. While that doesn't sound dark in and of itself (and the game has a fair amount of fun crack in it), the gamewide plots tend to be on the darker side--Asteroid M, HYDRA invading NYC, kids being hunted for entertainment by Mojo. Also, the mods run a pretty tight ship, so there's always plot to be had.
And then I co-mod Marvel United (marvel_united RPG which is an older Marvel movieverse game. Experienced players who are game for all kinds of plot. Since the game was founded at the very beginning of the Marvel Cinematic Universe: Phase One, we're currently in the process of folding in elements of the later movies, and we always love it when new players come into the mix things up. :)