Here's what I have in mind for the movie's premise. Remember, this is just what I want to see and the writers can come up with their own plot for the movie. Anyways, here's how I think it should go:

When Bunny has somehow come back to life looking like the rest of the Powerpuff Girls and being able to talk normally, the girls try to find an explanation for how this happened. Unbeknownst to them, almost all the villains in Townsville are banding together scheming to destroy Bunny! To make it worse, the Rowdyruff Boys have been banned from the big group scheme, so they try to start their own villain squad to top them by heading off to another dimension and teaming up with the Powerpunk Girls, who end up 1-upping the boys at every evil thing they do!