Dr. Horrible will be sidelined in the evil league of evil as he is spending too much time on a personal project... a device to bring Penny back. She is brought back, but I have no idea what next.... meanwhile Captain Hammer will possibly seek revenge on Horrible... I'm not sure on that one....
Prof. Normal and Dr. Horrible develop a loose friendship/partnership,being that they are the 'Super-Science' Villains. I think that both of them should be adverse to outright killing for killings sake. They are more interested in 'Teaching everyone a lesson'. Perhaps they, and other members of the ELE chaff under Bad Horse's iron hoof. They decide to break off and go their own way, but Bad Horse will have none of it. He pits the rest of the ELE against them, and quite by change both Dr. Horrible and Prof. Normal end up being labeled as Heroes by the press after thwarting a mass poising of the water supply planned by Bad Horse.(They enlist/force Johnny Snow to freeze the reservoir to make the poison inert.) Johnny is a better hero than Hammer(not by much though) and shares credit for saving the city with DH and PN. Add music and TADA!!