Doom: Repercussions of Evil/WMG

John is actually going berserk at a marine barracks, shooting his own comrades.
His own comrades are the ones who are shouting "He going to kill us!" The voice on the radio is a figment of his imagination. Cernel Joson himself is the one who said "I will shoot at him," and in fact shot John squarely in the body. John perceives the ceiling as having fallen on him because of the sheer pain of breathing or trying to move.

Cernel Joson is actually a demon cult leader.
He has been slowly corrupting John for 14 whole years. When it comes time to summon the demons, Cernel Joson encourages John to get closer to the demons, where he may then be corrupted and turned into a zombie.

John's father is actually a member of The Order from Silent Hill.
Their sect made a pact in which any descendant who leaves Earth will be available for consumption by the demons. John's father did not want to lose his only son this way, and tried to keep him on Earth by telling him half of the truth. Of course, John did not listen and so the demons came to collect.

The story is about how Ludd Was Right
The demons are representations of how technology and hierarchy crush the souls of common men. If only they stayed in their safe homes and lived according to the good old ways, they would be happy. Space ships, electric lights, military command structure, people with cybernetic implants, etc. all collectively compose the "demons" that kill John. When he is finally consumed by the evil modern technological world, his behavior is described as being like that of a zombie.

John is writing the story as he's trapped under the wreckage
The bizarre ending and nonsensical last half of the story is a result of lack of blood to the brain. The final sentence is an ironic statement of how he believes he will return to life as a zombie.

The demons are the one who resurrect John as a zombie.
John is a One-Man Army Blood Knight who slaughters his way through the demons, enough to make them actually scared for their lives. They manage to collapse the ceiling on him and kill him, but they realize how useful he would be as a minion, so they being him back as a zombie. Due either to their zombies being different or some other factor, John retains his consciousness, so he doesn't realize initially that he died - he's still focused on killing the demons, but when the voice on the radio tells him that he is the demons (let's assume that there was radio static, so the voice actually said "You are a pawn of the demons or something like that), he realizes that he can keep fighting even after death. As thanks to the demons, he makes a Face Heel Turn and embraces his zombieness.

John's dad was also a Space Marine, possibly the original.
At some point in the past, John's dad was responsible for killing or stopping the demons somehow. Afterwards, he settles down on Earth and starts a family, but he never forgets what he did. He knows that the demons were only temporarily stopped, and that they'll eventually come back. He tries to instill a fear of demons and space in his son, but it Goes Horribly Right - John believes in demons, but he's motivated to become a Space Marine to stop them. Thus, the titular Repercussions of Evil are that the demons were motivated to return to exact their revenge on John's dad, and converting John into a zombie is just icing on the cake.