Most Helpful Girl
I don't know what kind of story you're writing and what kind of power your protagonist has, but maybe try making the threat extend beyond the heroes? I mean maybe have a bomb detonate and hurt innocents or something like that.
You can also have the heroes caught in a trap of some sorts so they might get hurt?
You can also only make the protagonist think that lots of people will get hurt even if the villain can't really hurt anyone.
Also, maybe the villain in jail escaped and began hurting innocents.
I'm just not sure what kind of story you're writing..
Anyway, no matter what, make sure you foreshadow the surprise power your protagonist has so that it won't seem like a deus ex machina or lazy writing.