Well, I'm not sure what to do about that.
Perhaps a whole Carmen Sandiego + Sailor Moon thing.
1. Trying to follow/predict the path of the villain, picking up new friends and non-main-villain-related enemies along the way.
2. Sometimes arrive a bit too late, and pick up the pieces of what the bad guy leaves behind. Try to help recovering victims, build up destroyed things, solve mysteries, etc...
3. Sometimes arrive on time to track/stop/confront the villain's forces, but only occasional glimpses of the main villain. Mostly, though, it's his cronies and henchmen. And perhaps some undercover folks who seem benevolent, but plot underhandedly to take down the villain's enemies and extend the villain's rule.
4. Occasionally discover bits and pieces of information pertaining the heroes' past, and the villain's past, and keys to the villain's weaknesses, or favorite targets, or some attack plans, or whatever.
“…Judge not what a man has done, but judge what he could have done if he was a different bloke altogether. For art thou a leper? And a leper can changeth his spots…” --Rudy Wade, Misfits (Series 4, Episode 8)