Here's an idea - Let the players read the CoH comics from an ingame interface! They could go to a comic store or something, and even earn a badge for reading every comic! Maybe even have a know-it-all NPC in the store somewhere, who knows everything about the game lore - and will tell you anything you need to know about the history of Paragon City!
=D There could even be some mission arcs that start there, some hidden basement rooms that act as easter eggs, etc... I've actually got tons of ideas that are all completely unrelated lol... Another one is - when I first started playing CoH I was reading about contacts, and I misunderstood what they were and thought they were alter egos. But that would be awesome though wouldn't it? You could even let players actually work at their day jobs haha! Earn influence, temporary powers, badges, costume parts, recipies, enhancements, etc... Maybe even make it where you could do undercover work as a civilian? Like you could become a kidnap victim, and eavesdrop on your kidnappers - and get tips that way!

Or even join one of the NPC villain groups (Freakshow/Hellions/Circle/etc), and earn their trust to a point where they allow you the presence of their leader - and then you suit up and - THWAP! Whoop em. Lol I got lots of ideas but thats just a few.