The first full season of Matt Smith as the Doctor finishes with a sequence of episodes called “The Pandorica Opens/ The Big Bang.” The Doctor, Amy, Rory, and River Song are in Europe during the peak of the Roman Empire; an extraterrestrial prison, also known as the Pandorica, has manifested through the manipulation of Amy’s childhood. The Pandorica intended to house the most dangerous being in the universe. The twist of the episode is that the prison is for the Doctor. This is the first time the Doctor is portrayed as the likeable villain.
The Doctors greatest enemies from throughout all of time have teamed up in order to stop the Doctor for the last time. The audience gets to see how dangerous the Doctor appears to his enemies; his enemies go to great lengths to stop him. I personally love the idea of the Doctor being an “anti-hero.” It adds a different dimension to the Time Lord; he now is seen as a villain in a sense. It also adds a new layer to the motives of his enemies. For example, in this episode the Daleks are much more interested in stopping the Doctor than they are in eliminating humanity and taking over the entire universe.
Another instance in which we see the way people fear the Doctor is in the episodes, “A Good Man Goes to War,” and “Let’s Kill Hitler.” A group of people steal Amy and Rory’s baby because there were traces of Time Lord in its DNA. They condition the baby to be a weapon, and everything comes to fruition in “Let’s Kill Hitler” when River Song, who is Rory and Amy’s baby, attempts to kill the Doctor, saying it’s her mission in life. Over the course of Matt Smith’s tenure as the Doctor, the fear in which the Doctor instills in people manifests in brutal attempts to stop him. The Doctor may not be a stereotypical anti-hero, but in the eyes of his enemies, he’s their most dangerous villain in all the universe.