Pish posh.
It can most certainly have flavours of darkness, but it does seem to me to be predominantly about life before death (journey before destination, anyone? Heh. Ignore random reference.)
This speech kinda encapsulates that. It's certainly got darkness in it, but that's just to point out one thing - live, don't kill.
They also used to make a much bigger deal out of the doctor not using guns, and that's still there in the background - peace before violence.
Another example. The Doctor saves the lives of a galaxy(?). They were going to sacrifice a girl to appease a parasite-god, but he stops them. Flavours of darkness again introduced, with one overriding ambition; saving that galaxy and its lives. Hear them sing?
And another. He doesn't kill them; he lets them live. Still dark, though.
So yes, adventures and darkness galore. But at the very heart, the preservation of life.
To be fair, the doctor does kill the odd enemy/army. This is generally portrayed as a troubling and Bad Thing.
Sure the Doctor is all about preserving all life (I like the bit where he defends the AI murdering all the human colonists the moment he realized the AI had developed into a form of life, a form of life worth preserving shows this - it is an injustice, but he arbitrates it successfully to an uneasy reconciliation nonetheless). Hell, the Doctor himself desperately does all in his power to even save the life of his extremely dangerous nemeses (even trying to save the
master and
fucking daleks (and human-dalek hybrids), who are the reason his species his extinct). This is not exclusive to anything I say. That being the overarching ambition of the Doctor is not the same as the overaching theme of the series. The Doctor is not going from world to world in colourful festivals to teach the sanctity of life, he is going through time and space trying to preserve as much as he can in a universe that is destructive and dark. Goes to a Roman festival, it's fucking Pompeii. Doctor helps save colonists' lives, saying goodbye to little boy in heartfelt moment. Moment later, said boy has alongside the other colonists been forcibly turned into a warmachine in a body horror face-machine meld and set loose through time upon planet earth. All in the backdrop of running through time from a collective time abortion he is the last survivor of, though survivor suggests he was a lot more passive in that war than he was.
Haha, I don't need any more examples than this grimdark; there's a fucking great moment when Bill asks the most recent incarnation (which is, I might add, one of the most optimistic and idealistic incarnations we've yet seen) how many people he's seen dead. He doesn't know. She asks him, how many has he killed?
He doesn't answer. Saying only that he can't be outraged, because if he loses his good frame of mind, more people die. This is a dude who has killed billions, then killed them so hard they stopped existing. Not exactly the odd "enemy/army", he's killed billions of children, and one thing we've learned for sure is that "enemies" and "armies" are life just as worthy of protection, and yet he's wiped out so many that he had to forget (from dying many times) to move on. That's just numbers we know he knows, as since he's forgotten, we don't know the true extent of his destruction.
Shit's fucked. And the doctor churns through companions too for this same reason. He wants to protect them, wants to protect everyone, but he can't always and they die in horrible ways, heck IIRC The Tenth one tried to stop people joining him for a time out of guilt for how they'd end up inevitably killed (or as it were, trapped inescapably in alternate dimensions fighting a war). Twice when he traveled without companions, his tendency to sacrifice others increased, and of course when he has companions, they tend to end up sacrificing themselves in a rather regular pattern. In the end the Daleks are right, the Doctor is rather alike them, being the last remnants of the two time warring factions in a Universe that can't really stop them (seriously the dude fucks with time). That's why the story focuses on the real stakes: The companions, the humans, the cosmos's other lifeforms introduced, because the Doctor himself is this idealistic immortal time twister, the stakes come not in whether he'll be imperiled, but instead in whether he can protect this fragile world from the horrors it wreaks.
"Are you mad? You know the stories about the Doctor? The things that man has done? God help us if you make him angry!" - A good man goes to war.
"He never raised his voice. That was the worst thing. The fury of the Timelord. And then we discovered why. Why this Doctor, who had fought with gods and demons had run away from us. He was being kind. He wrapped my father in unbreakable chains forged in the heart of a dwarf star. Tricked my mother into the event horizon of a collapsing galaxy, to be imprisoned there forever. He still visits my sister once a year, every year. I wonder if one day he might forgive her, but there she is, can you see? She trapped her inside a mirror. Every mirror. If ever you your reflection and see something behind your mirror, just for a second, that's her. That's always her. As for me, I was suspended in time, and the Doctor put me to work standing over the fields of England as their protector. We wanted to live forever.
So the Doctor made sure we did." - The Family of Blood
I'd scarcely brush away the fact that wherever the Doctor goes, he is trying to keep the darkness at bay - this darkness is not a mere flavour dusted over the top of light hearted adventure and appreciation for life. This is the entity that put an end to the time war, that wiped out not just all the Daleks, but wiped out all of the Time Lords - including all of the Time Lords' children. He is beyond genocidal, he is apocalyptic, though slow to it I suppose. Consider that this is an entity that considered destroying the Universe in a cosmic suicide. Deepest lore m8, deepest lore
"You'll find that it's a very small Universe when I'm angry with you."Shit's fucked fam. If shit wasn't fucked, no one would be calling for a Doctor to fix it
*EDIT
Also if you really don't believe me, have the doctor gloating to the last survivor of a race he exterminated, his role as the architect of their death