Before I start I gotta make a little disclaimer: you prolly think "something's wrong with that dude, who gives a damn about STORY in DOOM?" Well yeah, you're on to something, but I'm just like that. I thoroughly enjoy and emphasize the story and setting of all games I play, however simplistic it is. Doom's no exception - I actually find what little of the story there is quite compelling. And of course I count only UD and D2 as canon, Final Doom not. Ok, so on to the topic:
Today I thought about making an attempt to make Episode 4 fit the continuum somehow. I know that it wasn't really supposed or expected to, given the circumstances of its creation, but I'm sure that with enough thought and retconning this could be done in a convincing manner.
So first: where the hell does it take place? Is it still in hell? Back on Earth already? Is it an anomalous dimension linked somehow to the portal through which the Marine returned from Hell to Earth? Well, my take is such: the orange skies suggest that the episode is taking place on Earth already. Most likely in a stronghold of Hell built on Earth, just outside of the portal. Though the intermission screen after Inferno says that the marine saw "the green fields of Earth", obviously a fourth episode hadn't yet been thought of. So it's a Hellish stronghold built by the invading armies upon Earth, probably to safeguard the passage between Hell and Earth to facilitate their invasion. And that's a distinctly different location from the portal that's mentioned in Doom 2, the one that takes one to the other side of the infested starport.
Second: Why is this so populous, while even Hell itself was comparatively empty? This one's actually quite easy to explain. Hell itself never expected an invasion upon it, and it was Hell itself that launched invasions upon other planes. Therefore it stands to reason that Hell's armies stationing in Hell itself would be only adequate. On the other hand, an army devoted to a grand invasion like that of Earth would have to be superb in numbers. Earth is not only incomparably larger than either Phobos or Deimos - it is also incomparably more populous. Hence, invading forces would have to be much, much larger. And what better place could there be to put many of them than the first stronghold you build on Earth? I say the Thy Flesh Consumed levels host the bulk of the hellish troops poised to strike outward, yet devoted to guarding the interplanar portal.
Third: What's the Spider Mastermind doing back alive? Well, actually it's not a stretch to assume that this Mastermind isn't the same one that died in Dis. It's just another Mastermind sent to Earth to oversee the initial stages of the hellish invasion. Hence, a very appropriate object of Doomguy's revenge for killing Daisy - it's without the very horde it was leading that caused the poor rabbit's demise.
Ok, that's all I can think of for now. Please add something if you can even be bothered to give any thought to that kind of stuff.