WMG / Doom Three

The Doomguy in Doom 3 and in the Resurrection of Evil Expansion Pack were both named "Marine."
Evidence for this lies in the fact that nobody, throughout either game, calls them by any else — except in the ending sequence for Doom 3, in which he is referred to as "Corporal" by someone who has no way of knowing his name! Furthermore, the marine in Resurrection of Evil is referred to more directly as "Marine" by Dr. McNiel. This implies that they are related; perhaps the Resurrection of Evil Doomguy is an older brother or cousin.

The protagonists had help.
Seriously — how easy would it have been for the forces of Hell to simply keep sending an infinite number of enemies until the character was overwhelmed? Or turn the two protagonists into zombies, as they had with every other soldier on the base? In fact, the hellish "visions" received throughout Doom 3 were just such attempts to zombify the main character — but they failed due to some sort of intervention, either divine, or by some opposing faction at work in Hell, or some other force which was opposed to Hell's invasion of Mars but couldn't or wouldn't work openly.
  • Maybe the first Doomguy? He gave aid from... An Alternate Universe!
    • Every time the first Doomguy missed in the first two games, he wasn't actually missing his targets. The shots crossed dimensional boundaries, went to the Doom 3 reality, and killed the demons there. It's the only reason he "missed" at all.
  • Considering that it can be accurately described as a "sentient weapon", maybe it was the Soul Cube (or specifically, the souls that helped create it/inhabited it).
  • Maybe it was Alma! (see below)
  • As there is nothing to say this isn't possible, maybe it was an immortal, even more badass, Willow.

Alma is on Mars!
In one of the Alpha Lab levels, if you enter a side corridor you hear a creepy female voice whisper "They took my baby." followed by a scream and some paranormal activity. The voice is eerily similar to Alma's, who says pretty much the same thing to you at the end of F.E.A.R..
  • The voice also unlocks a hidden closet full of ammo for you after spooking you a bit, which suggests it's on your side and opposed to the Hell Forces. Perhaps Alma doesn't like competition.

Doom is a playable segment of ancient history within Warhammer 40,000
Experiments in teleportation involving trips to hell, check. Demonic possession and corruption, check. Chainsaws, check. BFG's, check. Badass Normal taking on the daemons with guns and winning, check. The list goes on...
  • Heck, that even gives a reason for the marine's edge. Pariah gene, anyone?
  • There are two missing Primarchs, given the amount of daemon ass that gets kicked...
The Doom 3 Marine died in the initial attack and went to an Ironic Hell
The hell being endless corridors filled with demons and monsters and no hope, his only human contact the PD As of people he had already blasted. And the occasional hiding human.

The Marine is a direct descendant of the Martians.

In the latter levels of the game, there are several theories that suggest the Martians who survived the demonic invasion and didn't sacrifice themselves to create the Soul Cube fled to Earth. The Marine could very easily be a descendant of those refugees, for a couple reasons shown in the course of the game:
  • Betruger's interest: Betruger really couldn't care less about most of the marines in the complex, sending swarms of lesser demons (Imps, Wraiths, etc.) to finish them off. But note that a) More powerful enemies appear to challenge the Marine on his journey through the facility, and b) the areas of the facility that (literally) go to Hell as soon as you get near them. It's possible that Betruger somehow knows (via the demon he hosts, maybe?) that the Marine isn't a mere human grunt, thus he tries to slow him down/finish him off at every opportunity.
  • The Soul Cube: When you reach the part of the Delta Labs where they were analyzing the Soul Cube, you can hear the scientist talking about it in a PDA audio log. In that log, he says they've deciphered what the markings on its exterior say, but they cannot get it to activate in any manner. Yet, when the Marine reaches the Guardian in Hell, it's activated (with spinning blades and everything), and it's speaking. This would imply that it only activates when a) an invasion by the demonic forces has begun, and b) it senses that there is an individual nearby who is Martian/of Martian heritage. It would give a new twist on why Betruger took the Soul Cube into Hell in the first place. Not only would the demons have possession of the most powerful weapon that could be used against them, but the high chance that the Marine would be killed while fighting through Hell could guarantee that no one could recover it until it was too late (ie, the demons have retaken Earth).
The Martians are the Ancients
  • And the Hellportal is a prototype of the Stargate. Think about it the Stargate Universe gate spins while dialing, the Hellportal spins the whole time it's on, perhaps to keep the established connection with Hell active. And then once the Ancients found a better way to make portals, they abondoned the Hellportal for the Stargate.
Betruger is an Ori
  • He has sunken in eyes and one of his eyes are bright fuckin' white, plus he's power hungry, pale-skinned, and want to make Hell be everywhere and kills anyone who gets in his way.

The Doom 3 Marine is B.J. Blazkowicz revived from cryogenic stasis, and Betruger is the reincarnation of "Deathshead" Strasse.

Depending on which continuity you go with—with the series either ending with Wolfenstein 2009 or with the alternate history of The New Order—B.J. Blazkowicz volunteered to use the technology recovered from Castle Wolfenstein to have himself frozen in cryogenic stasis, to be awakened if the technology should ever be used to threaten mankind again. Centuries later he was found in the castle ruins by Union Aerospace forces, but the degradation of his capsule caused problems with his revival, which cost him his memories. The executives of the UAC—having known of Blazkowicz and his history—immediately saw the potential use for him as a one-man army, and he was trained in the elite military under the name John Kane. One single act of defiance led to his transfer to Mars City, something Betruger didn't expect...

Dr. Malcolm Betruger not only bears a bit of resemblance to Wilhelm "Deathshead" Strasse—bald old scientist with two different eyes—he also shares Strasse's brilliant mind and keen affinity for research and development. Betruger is also a German-sounding name. When Betruger first entered the portal to Hell found in the ruins on Mars, he came face to face with the vengeful spirit of "Deathshead", who the Icon of Sin had given command of its demonic armies for its invasion of the mortal realm. "Deathshead" possessed Betruger and was fully reborn in his body, sent to open the gates of Hell and unleash the invasion. The one thing "Deathshead" hadn't counted on was his old enemy—the amnesiac B.J. Blazkowicz now known as John Kane—being transferred to Mars.

If you're going with the Doomguy's name used in the Doom RPG, then somewhere along the line B.J. possibly got his memories back and met a woman who he started a family with. This would eventually lead to Stan Blazkowicz, the Doomguy, who would continue his predecessor's battle against the forces of Hell.

The 'They Took My Baby' woman is a complete deception.

There never was a woman with a baby, or at least one that the player encountered. The signs of one, including the ammo stash reward, are traps for Human males hard-wired culturally to hear this sweet-voiced young mother call on them and respond with instant go-getting. But Doomguy was different. Very willing to help, but not rushing in without checking the terrain. Now, this isn't putting harming a child past these forces - its possible the demon pregnant with a mancubus was once a Human mother and infant, and a horrific bloated corpse on the wall near the final battle could be a late infant - but this particular set-up—was a set-up, and once Doomguy took it slow (as gameplay almost requires), the trap's value was gone.