Dr. Horrible is, at his core, two things: a nice guy, and a villain. His belief is that “the world is a mess, and he just has to rule it,” which stems from his dissatisfaction with the state of society's frustrating power structure and tendency of cutting off support from the people who need it most. Ultimately, his decision to become a villain reflects just how much he <i>cares</i> in a roundabout way: if the system is corrupt, then the fastest way to fix it isn't going to be found inside it. It would be like trying to use one of those fake really-a-virus antiviral programs to get rid of another virus. So, he wants to bring in something new, something... evil, if only in name, and rebuild a more positive society. To that end, his goal is to enter the Evil League of Evil, one of the most prestigious evil organizations in the world, and in doing so better his villainous standing and increase his chances for success. His drive to do this is similar to a student trying to get into college, a youthful determination to make his dream come true, but his lack of ruthlessness seems to pose a problem. He is unusually scrupulous for a villain, wishing to avoid harming innocents in his conflicts, to the point that part of the reason he avoids a fight in a particular park is to prevent putting children in that park at risk.

Indeed, outside of his secret identity of a villain, “Billy” (perhaps Dr. Horrible's true name, perhaps another alias) is quite mild-mannered and shy. He shows extreme awkwardness in social situations, such as his attempts at communicating with his crush, Penny; it takes him a very long time to come up with even a slight “real audible connection” between them, where he avoids mumbling. And then he does it almost by accident, when he's startled. He slips into nonsensical similes or simple stammering easily, and generally has trouble communicating his ideas in a straightforward manner. He regularly second guesses his speech and actions, often finding himself at a loss around other people, but is generally well-meaning despite his uncertainty. He is given to act hastily, often saying things before really thinking about them, such as when he tells Penny that he admires Bad Horse, the “thoroughbred of sin” who rules the Evil League of Evil. It can, however, be said that he wants the best for those he cares about, even if he's not always sure how to go about getting it, with or without the help of some diabolical weaponry.

He is fairly quick to anger, but does not often display that irritation in any particularly extreme way. This is mostly shown when he interacts with his nemesis, the hero Captain Hammer. When aggravated by Hammer and others, Dr. Horrible reacts with undisguised annoyance, along with a healthy dose of sarcasm. This can actually be taken as a degree of courage when Hammer is involved, if not one that he thinks much about, because Captain Hammer is much stronger than him, and has beaten him up rather nastily more than once, but Dr. Horrible continues to persist in his efforts and behave with open contempt for the corporate tool. He often snaps at people who bother him, sometimes not really intending to react quite so bitterly, and makes himself nervous and apologetic in turn.

His hammy villain behavior does not cover up his genuine motivation or kindness, as he will speak wistfully of becoming a real supervillain for positive reasons, but becomes defensive and anxious at suggestions of more serious violence. But despite this, he certainly displays more than his share of a villainous attitude. The evil laugh is matter of principle for him, and he is in the midst of working on a catchphrase with which to appropriately represent his evil identity. It seems to provide a somewhat easier means of expression for him, allowing him to voice his hopes for the world through his blog. The persona seems to grant him significance, or at least the potential to become significant, and he is not inclined to hold back on his evil deeds (as long as no kids gets hurt, of course) because of his determination to see improvement in society through the power they give him in the long run. As awkward and shy as he is, Dr. Horrible gives him the chance to make a difference, as so many people wish to. Even if his methods are a bit unconventional.

Generally speaking, Dr. Horrible will attempt to put on his villainous front, though he may venture out as Billy if a situation requires it. So, though he will seem evil at first simply because he will openly state that he is, people who get to know him will discover the awkward but nice enough guy underneath. A failure of a villain, but a hard worker who wants the best for everyone, and hey, if evil is the quickest way to make people happy, he doesn't have enough faith in society to object.  He is loyal to his friends, sarcastic to his enemies, and loves frozen yogurt.