Dr. Horrible is the primary character of Dr. Horrible’s Sing-Along blog.
He seeks to use his inventions to take over the world so he can enact positive social change. To this end he wishes greatly to join Bad Horse’s Evil League of Evil.
Our story starts as Dr. Horrible is filming an entry for his video blog, giving updates on his schemes and responding to various emails from his viewers. His friend Moist delivers a letter from Bad Horse, leader of the Evil League of Evil which lets Dr. Horrible know that his petition is being evaluated and that the League will be watching for his next heinous crime.
In his secret identity of ‘Billy’ he has a crush on the generous and giving Penny. The two had never spoken until Dr. Horrible sought to steal wonderflonium to complete his freeze ray. Penny interrupts Billy as he attempts to take over control of courier van that is transporting the wonderflonium. She asks if he would sign her petition to save a building for a new homeless shelter to which he is aloof and rude about homelessness being a symptom of a larger problem primarily that the world’s power should be other (his) hands. He signs and becomes distracted with his heist and she leaves thinking he is somewhat rude.
Billy regrets being so rude but focuses on the task at hand, controlling the courier van, but suddenly out of nowhere Captain Hammer appears on the top of the van and damages Dr. Horrible’s control device sending the van careening out of control. Captain Hammer leaps off the van completely oblivious of the danger to the bystanders. The van turns a corner and is about to run down Penny, but Captain Hammer shoves her out of the way even as Dr. Horrible is finally able to command the brakes to halt the van, stopping it just short of Captain Hammer.
Dr. Horrible comes out of hiding to confront Captain Hammer for endangering Penny, but Hammer merely grabs him by the throat and slams his head into the hood of the van even as Penny emerges from the piles of trash that Captain Hammer shoved her into thanking him for saving her life, and shows signs of being enamored with Captain Hammer, which greatly frustrates Dr. Horrible that they’d be so ignorant of what just happened. While they are so distracted with each other he takes the wonderflonium and walks away in disgust.
Dr. Horrible stalks Captain Hammer and Penny on their date. Dr. Horrible is clearly depressed while Penny is obviously falling in love with Captain Hammer, and Captain Hammer is just happy that he may get laid. Meanwhile at the Landromat, Billy and Penny are forming a fast friendship despite that Billy is clearly not taking Penny’s relationship with Captain Hammer very well.
On his blog, Horrible reveals that his Freeze Ray has been completed, and that he plans to use it the next day. The following blog post reveals that he has failed, as Hammer and the LAPD watch his posts, and they were ready for him. Captain Hammer threw a car at his head. Dr. Horrible receives a call from the Evil League of Evil saying that since he was humiliated by Captain Hammer that he must kill someone. Dr. Horrible is conflicted over it since he’s not a killer.
Later, back at the laundromat Penny and Billy talk about his problems and the possible job offer he has. Penny mentions that Captain Hammer will be dropping by and Billy panics and attempts to leave only to bump into Captain Hammer. Billy feigns having never met Captain Hammer before and Hammer explains that he got the Mayor to cancel the demolition of the building that Penny was trying to save for the homeless. Penny is terribly excited and she excuses herself to switch laundry loads. Billy goes to leave but is stopped by Captain Hammer who admits he does recognize him and that he’s only going to sleep with Penny just because Billy has a crush on her. So that he can have what Billy wants. It is then that Billy decides to kill Captain Hammer.
L.A. is abuzz with Captain Hammer's crusade to help the homeless. Penny waits at the laundromat to share frozen yogurt with an absent Billy; and Dr. Horrible works diligently to refit his Stun-Ray into a Death Ray.
At the opening for the new shelter, Captain Hammer begins a speech praising the homeless but it degenerates into a praise of his own excellence and relationship with Penny. Penny tries to leave, but is interrupted by the appearance of Dr. Horrible, whom she recognizes as the man she knows as Billy. Captain Hammer is frozen by the Freeze Ray, but Dr. Horrible, now armed with a death ray, hesitates when trying to kill him. In Horrible's moment of hesitation, the Freeze Ray unexpectedly fails and a revived Hammer knocks him across the room, damaging the death ray. Horrible attempts to warn Hammer about the broken death ray, but Hammer disregards him. Hammer then turns the damaged death ray on the now helpless Horrible, but it explodes in his hands as he attempts to fire. Injured by the blast, Captain Hammer feels pain for the first time, cries, and flees, a gibbering wreck. Penny is hit by shrapnel and dies in Horrible's arms, deliriously reassuring him that Captain Hammer will save them.
In the wake of the death of Penny and the defeat of Captain Hammer, Horrible becomes a member of the League. Afterwards, Billy tearfully posts on his blog that he "won't feel a thing,".