The city is abuzz with Captain Hammer's crusade to help the homeless and he is considered the city's new hero; Penny ponders her relationship with Captain Hammer, waiting at the laundromat to share frozen yogurt with an absent Billy; and Dr. Horrible goes into seclusion while obsessively constructing a Death Ray to kill Captain Hammer once and for all ("So They Say").
At the opening for the new homeless shelter, where a statue of Captain Hammer will be unveiled, Captain Hammer begins a speech of encouragement to the homeless, but it degenerates into selfish, condescending praise of his own excellence and relationship with Penny ("Everyone's a Hero"). Penny, embarrassed and disillusioned, quietly tries to leave as the crowd joins in singing Hammer's song, but they are interrupted by the appearance of Dr. Horrible, who uses the Freeze Ray on Captain Hammer, cutting his song short. Dr. Horrible taunts the shocked crowd and declares that they cannot recognize that Hammer's disguise is "slipping", and he reveals a second, more lethal laser gun: his completed Death Ray ("Slipping").
At last, Horrible aims the lethal weapon at the frozen form of Captain Hammer, but hesitates. At that moment the Freeze Ray unexpectedly fails, and a suddenly revived Hammer punches Horrible across the room. The Death Ray falls from his hands, damaging it. Hammer then picks up the Death Ray, turns it on Horrible, and triumphantly completes the final note of his prior song. However, ignoring Dr. Horrible's warnings, Hammer pulls the trigger and the damaged Death Ray misfires. The weapon explodes in Hammer's hands, injuring him and causing him to feel pain, apparently for the first time in his life. He flees, a wailing wreck, asking for "someone maternal." Dr. Horrible realizes suddenly that he has succeeded in vanquishing his nemesis, but still having not committed the murder required by the League. Unfortunately, he discovers Penny slumped against a wall, gored by shrapnel from the exploding gun. Tragically, she dies in Horrible's arms, deliriously reassuring him that Captain Hammer will save them.
Dr. Horrible declares Pyrrhic victory, with "the world [he] wanted, at [his] feet," seeing that her death is ironically the murder he required. In the aftermath, Horrible gains infamy and is free to commit additional crimes unfettered by Captain Hammer. Horrible becomes a member of the League, striding into a party in celebration of his induction, attended by Moist and the villains Pink Pummeller and Purple Pimp. Captain Hammer is seen on a psychiatric couch sobbing to his therapist. Dr. Horrible, donning a new outfit – red coat, black gloves and his goggles covering his eyes – takes his seat at the League, composed of Tie-Die, Snake Bite, Professor Normal, Dead Bowie, Fake Thomas Jefferson, Fury Leika, and Bad Horse (an actual horse). He addresses the camera, saying, "now the nightmare's real," and in working "to make the whole world kneel," that "[He] won't feel...". He completes the line "...a thing," in a final blog post as a numb-looking Billy, out of costume and looking lost in the midst of his lab. ("Everything You Ever")
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