1. Dr. Horrible (Billy) is an evil mastermind.
2. He wants to get into the Evil League of Evil (that is, by stealing Wonderflonium)
3. He steals it, while inadvertently introducing Captain Hammer to Penny.
4. He deals with their blooming relationship, while the ELE tells him he now has to kill someone.
5. Solution: try to kill Captain Hammer.
6. Penny dies which, ironically, will grant Dr. Horrible into the ELE.
7. Dr. Horrible returns to causing ruckus, but strangely conflicted.
8. ELE admission at the cost of Penny makes it a hollow victory. He shuts himself out from the feeling