The Doctor defeated the Daleks and destroyed the Time Lords by ending the Last Great Time War. It's been stated in the show that The Doctor doesn't always act heroically, and has killed in the past. Sometimes, The Doctor doesn't even see themselves worthy of their title, hence the long-forgotten War Doctor incarnation.
Although our favourite Time Lord has always tried to find non-violent means of dealing with a situation, that doesn't mean they haven't acted on their darker side and resorted to killing. Sometimes this is for the greater good, sometimes it's killing enemies such as the Cybermen or the Daleks, and sometimes it really is unavoidable for The Doctor.
The Doctor often preaches against the use of guns, and is always anti-war, that's because they have fought in a war, and therefore developed a much darker side than we're used to seeing. Although The Doctor often acts in a way that would make us want to be their best friend, there are times when the mask slips, and we see the fury within. So, here are The Doctor's 5 Darkest Moments.
5. Colonel Runaway
The Eleventh Doctor amassed an army of allies in order to take on the Kovarian Sect of The Silence, and rescue Melody Pond. The Doctor infiltrated the ship, and posed as one of the Headless Monks. He then revealed himself as the Colonel rallied his troops, and sent the room into chaos.
Although the Colonel was regaining control of the room, The Doctor ensured that the Colonel was unable to completely recover; whilst The Doctor's allies revealed themselves and outnumbered the Colonel's forces, he spoke to the Colonel directly.
The Doctor instructed the Colonel to order a retreat; but not just this, he wanted the Colonel to tell his soldiers to "run away." In doing this, The Doctor humiliated the Colonel in front of his troops, and ensured that little children would find the leader's home and name him as "Colonel Runaway." This was a truly dark moment, and earned the location the phrase: "Demons run, when a good man goes to war."