For a hero, the Doctor does an awful lot of bad things. From destroying entire civilisations to leaving children to die on the battlefield, he’s hardly a goodie blue-shoes, and sometimes seems to cause more harm than good. Even the Doctor is sometimes compelled to ask:
Let’s consider the evidence.
Who's to blame?
Imagine you’re a bit player in a Doctor Who story. There you are, living happily in your 15th century village, making hay, chewing cud, when suddenly a strange man shows up. Around the same time, all of your friends start dying.
What conclusions would you draw? You can’t really blame the terrified locals for throwing him in the nearest dungeon every episode, can you?
The Doctor’s habit of arriving just before trouble strikes has often been remarked upon (and it’s kinda-sorta-canonical that the TARDIS deliberately lands at trouble spots) but the Doctor would argue that just because bad stuff happens after he showed up, doesn't mean he caused it. This is a fallacy known as post hoc ergo propter hoc. If you were on the TARDIS or in Ancient Rome, that would translate as "after it, therefore because of it".
However, whether he helped cause the initial problem or not, it’s undeniable that in the course of trying to save the day, his actions often directly result in deaths, sometimes many, many deaths.
For instance, in the Fires of Pompeii the Doctor deliberately causes Vesuvius to erupt, killing almost the entire population of the Roman town, in order to prevent an invasion of rock people.
Now, we’re no fans of rock people, but how can killings thousands of people ever be the right thing to do?
Only following orders
One possible answer is that the Doctor is sometimes forced into ‘bad’ or unpleasant choices through circumstance.
For one thing, the Doctor is a Time Lord, with power and duties we can barely grasp. Perhaps his primary responsibility isn’t always to do the right thing, but rather to maintain the integrity of history. Pompeii had to explode, or time would fracture, and it’s the Doctor’s job as a Time Lord to ensure that doesn’t happen.
The question is, why?
Well, for much of Doctor Who’s history, the Doctor was outranked by a council of Time Lords, who would sometimes send him on missions. Sometimes these orders were morally dubious. In Genesis of the Daleks, the Doctor was told to wipe out an entire species – a grim task, even when the species in question is your mortal enemy.
In this case the Doctor didn’t go through with the order, but if he had he could claim to be "only following orders". However, these days we tend to take a dim view of the so-called ‘Nuremberg defence’.
But then we all know that the Doctor was never one for following orders. No one could make him do anything he didn’t want to do. His decision to destroy Pompeii was his own.
Perhaps the simplest explanation for why the Doctor does bad things is the best one: it’s to prevent something worse. For instance, not following the course of history – by, say, saving Rose’s dad in Father’s Day or the Doctor in The Wedding of River Song – is seen to cause universe-ending paradoxes, killing billions.
In that case, allowing one person or a relatively small group of people to die is surely justifiable, as it stops a much larger group of people coming to harm?
This is the most frequent moral quandary the Doctor faces. In The Beast Below, he decides that lobotomising an innocent Star Whale is necessary to preserve the civilisation that lives on its back. (The fact it is a ridiculous problem doesn’t make it any less wrenching.)
One of the Doctor’s defining moments was his (apparent) use of the apocalyptic weapon The Moment to end the Time War – this time actually killing the Daleks and the Time Lords – in order to stop more civilians dying in the fighting.
This is a form of Utilitarianism – a branch of moral philosophy whose most famous fan has pointy ears.
A similar rationale was used to justify Harry Truman dropping atomic bombs on Hiroshima and Nagasaki – with many arguing that the loss of life was justified as it forced Japan to surrender, preventing World War II from dragging on and ultimately killing even more people.
Utilitarianism is a consequentialist philosophy, which argues that it’s not the action itself, but the effect of an action that counts. Put another way: the end justifies the means.
So, in some cases the Doctor is choosing the lesser of two evils, but why does he have to choose either? Why can’t the Doctor keep his hands clean, and take no action at all?