This franchise has been around over six decades now, and there are some stories which really push the boundaries of how dark and depressing and generally horrific you can go.
So I wanted to know what you consider to be the darkest stories?
I’ll kick things off:
I don’t think anything in the Whoniverse gets much darker than Children of Earth.
Miracle Day isn’t much better when you think about it. That politician who is crushed into a cube with a car and you can see her eye moving, so she has some degree of awareness and there are months left before the end of Miracle Day!
Plus the whole thing with the convicted pedophilic murderer
Shudders
I think CoE is worse because of how it directly involves children. The bit where they are bussed away… 
It is so painful to watch!
That scene literally made me sick to my stomach.
And when Frobisher closes the door on his own family with a gun in his hand.
Aside from the aforementioned Children of Earth and Miracle Day, Torchwood also has the audio Corpse Day. I’m not a huge fan but it definitely qualifies as one of the darker Doctor Who stories.
It does make me wonder what qualifies of stories actually featuring the Doctor. Looking it up online Midnight and Waters of Mars were mentioned for the new series. Earthshock and Caves of Androzani were mentioned and I agree fit. Scherzo, Natural History of Fear, Lucie Miller, and To the Death for audios. I don’t know these audios as well, but have found the stories leading up to Scherzo like Seasons of Fear pretty dark.
Though not necessarily that dark in comparison to the broader show, considering it was very much a kids show, watching stuff like Whatever Happened to Sarah Jane? (persuading your best friend who died as a teenager to sacrifice herself all over again) and The Curse of Clyde Langer (everyone hates you to the point where you become homeless and meet a new friend who seems to never have existed at all) are two of the SJA episodes that come to mind as pretty dark ideas
Should this post be merged with Dark Doctor Stories?
I think there’s enough of a difference between the two.
This is about the stories in general, my thread was specifically surrounding the Doctor’s character, those two things feel separate enough to be two different threads.
And let’s not forget how Jack saves the day.
By murdering his own grandchild.
I love when Doctor Who goes dark with its stories.
I feel I’m obligated to mention all of Shearman’s audios, except maybe Chimes, that’s not exactly dark.
Nightshade was surprisingly grim (Everybody dies!), as was Love and War
Protect and Survive is gloriously bleak and horrifying
Pretty much all of Only the Good and I assume the whole War Master range, though I haven’t listened to them.
Dalek, Turn Left, Midnight, 73 Yards all did some pretty messed up stuff to its characters.
Just some I thought of off the top of my head
Fair enough. I just vaguely remembered a very similar thread so I looked it up.
I don’t know if there’s an episode of the War Master range that doesn’t fall into this category
I don’t know that the story as a whole is much darker than others of its time, but Image of the Fendahl has a pretty bleak ending: Fendelman realizes he’s in the wrong and tries to stop the ceremony, only to be shot by his supposed protégé, Stael. Moments later, Stael in turn realizes he’s in the wrong and that there’s no way out, so begs the Doctor to help him commit suicide. Which the Doctor does, because it’s honestly the kindest thing at that point.
And Thea, who’s totally innocent, is forcibly turned into the big bad, and as a consequence isn’t even present for her own death.
Great episode. One of my favorites, and I’m not kidding.
A number of Torchwood stories certainly fit this bill; one I haven’t seen mentioned yet is the audio episode Hostile Environment. The Bernice Summerfield audio Closure is extremely dark as well. In mainline Doctor Who, however, the darkest story I’ve come across is the New Adventures novel Eternity Weeps by Jim Mortimore. Imo it’s up there with some of the most depressing of Torchwood.
Torchwood at Big Finish can be dark as hell sometimes.
Propoganda - at the end of the day the plot is about trying to create intrest in a bioweapon that can be selective based on ethnicity. And the fact that it seems plauseable nations would it, is very bleak.
At her Magesty’s pleasure- a woman is locked up for life in Yvonne’s place just for doing her job. Its very sinister even if its not super dark the performance is chilling enough that it works.
As DispersalPhase mentioned, Hostile Environment is very dark in a very down to earth way.
Mother’s Son - A woman choosing to forget her dead son as the loss is too much is just heartbreakingly sad.
Colin Alone - I mean the way it basically breaks Colin down is so depressing. However Colchester at the end swooping in does end it on a positive note unlike the other stories mentionied.
I think when done right Torchwood is inherently dark, i think every boxset theyve done has at least one.
One of the darkest (and best) Doctor Who stories in my eyes has to be Palindrome. The way we see a Davors who is ultimately a flawed but good man get corrupted by the daleks to the point where he kills his wife is chilling
At the end of the day most stoires have some dark elements, it’s just what affects us personally the most that makes some darker.
We also have Things that go bump in the night from a while back that is kind of similar to this thread 
Why would you kid about that anyway? Image of the Fendahl is absolutely amazing 
This is one that I wish got discussed more. That being said, I think I’m biased towards ‘Protect and Survive’ because it was very clearly inspired by a film from the 1980s.
One of my favourite films of all time actually.
Two words - Project: Lazarus
Also, The Shadow in the Glass. It has an unexpectedly dark ending
