Karen is cornered in the subway station by demons that have emerged from the bodies of the slain. All the religious believers have committed suicide to flee the final judgment. Karen closes her eyes for a moment and when she opens them, she smiles.
Karen (Ilona Elkin) is a nurse working in a psychiatric ward. The patients she treats have become more violent and delusional, claiming the end is near. Worse yet, some of the patients are drawing pictures of anarchy and demons that Karen herself is beginning to see. One of the psychiatric patients who is released kills herself by jumping in front of an oncoming subway car.
Her hospital is full of signs, posters and donation jars for a religious group called Voice of the Eternal Hope led by Reverend Hope. We watch as Karen gives a donation and takes one of the muffins the group bakes themselves and provides in exchange for a donation. Karen eats the muffin and then leaves work, heading to the subway where her former patient was killed. While waiting for the train, she sees a vision of her now-dead patient and is harassed by a church member named Patrick (Robin Wilcock). Another man named Mike (Nicolas Wright) steps in to help Karen and Patrick slinks away. When the train arrives, all three board (and the train is full of members of Reverend Hope's Church).
While on the train, Patrick finds a girl named Julie (Emily Shelton) alone in one of the cars and hits the emergency stop button (thus cutting out the power) so he can have some time to try and rape her. The conductor interrupts them and after he leaves, she pepper sprays him and runs off. In another car, a girl (actually a member of the Church) named Sarah (Nina Fillis) has sex for the first time with her boyfriend John (Tim Rozon). When the electricity is restarted by the conductor, all of the Church-members on the train (of which there are many) receive texts. The texts cause them to take out bladed crosses and begin killing every non-Church member in sight. Only Karen, Mike, Julie, Sarah, John and a tough guy named Neil (Neil Napier), who was friends with some of the Church members, manage to get off the train alive - though Mike is wounded. The Church members pursue them, led by one of the Church elders named Betty (Joan McBride). They claim the apocalypse has come and that they are killing people so their souls may rise to Heaven before Satan's demons appear on Earth. Sarah sticks with the group as she is in love with John.
The group eventually meet two subway workers named Davis and Frankie who let them take shelter in a storage room. They discover that the TV, radio, and phone lines are down. They theorize that Reverend Hope has simply managed to violently take control of the city's communications. The group finds tools to arm themselves and all but Davis and Frankie (who prefer to try and wait it out in the storage room) leave to try and make it out of the subway tunnels and to the surface. It is later revealed that Frankie is a Church member, though he has no desire to kill. Betty and her acolytes eventually make it in to the storage room and kill Davis. They then kill Frankie and his pregnant wife (who had come to the subway to find Frankie and be "released" from the world with him and her baby). It is also revealed that all of the Church-members have been eating nothing but the Church-baked muffins for the last few weeks.
The group is accosted as they journey through the tunnels, even having to kill a child who is a member of the Church. John is seriously injured and both Karen and Sarah begin to see demons (none of the rest of the group does). They make it to a control room only to find Patrick has killed everyone there. They take Patrick hostage and try to gather their strength. Karen and Mike have a heart-to-heart, where Mike says that if ghosts and demons exist, he would smile and be happy no matter how scary it is as it means that an afterlife exists (or, he explains, it may mean that you have lost your mind). John can no longer walk, so the group is forced to leave he and Sarah behind (promising to send help when they reach the surface). Patrick manipulates Sarah into freeing him and kills John. He tries to rape Sarah but is interrupted by Betty. Though she gives Patrick a reprieve, she kills Sarah for breaking her vow of chastity by sleeping with John.
The group gets near the end of the subway tunnels when they are attacked again. Though they kill all the members who found them, Mike is wounded again. The group agrees to let Neil go to the surface to find help, and when more members show up, Mike convinces Julie and Karen to leave him too (although they are separated while being chased). Mike is not killed as the Church-members believe he is already dead as he passed out from his wounds. When Neil reaches the surface, he finds rioting, fires and destruction on the streets. Standing in awe of the apparent apocalypse, he is stabbed by Betty who snuck up on him. She cradles him until he dies - having delivered him to god.
Meanwhile, a bunch of Church-members have cornered Julie and Patrick has cornered Karen. Suddenly, the Church-members get another text and they stop their assault. They then feed each other cyanide pills and die (suicide being a sin, they technically "kill" each other by feeding each other the pills. Julie is left lost in the tunnels after the Church members kill themselves, and soon the electricity and her flashlight die (we never see her again).
Patrick has ignored the text, however, lamenting that he has neither seen demons or angels despite his devotion. Betty shows up and tries to get him to feed her the pill, but he stabs her instead, forcing her to commit suicide if she wants to die before the demons arrive. He then says he refuses to die a virgin and tries to rape Karen, but she manages to bite off his lip and then fatally stab him with his own knife. Meanwhile, Mike recovers and tries to make his way to the surface when he encounters a Church Member who had noone to feed him the pill. The Church Member goes towards a defenseless Mike, but then runs away from something that is behind him (the viewer never sees what, if anything, is behind Mike).
Karen is sobbing on the ground after her ordeal, when she sees demons beginning to surround her. Two demons emerge from the corpses of Betty and Patrick (the Church had said that Satan would use the bodies of those remaining on Earth to bring forth his demons). They corner Karen who initially screams in terror. The camera remains solely on her face as she opens her eyes to take another look, and what she sees makes her smile (the viewer does not know what she sees when she re-opens her eyes, but there is a shadow on her face).
There are a couple likely explanations for this. The most obvious is that she remembers Mike's statements that demons simply signify that an afterlife exists, and takes his advice to rejoice in such knowledge as her death will not be the "end" of her. In this interpretation, the Church are "heroes" in helping to spare people from the apocalypse. In the director's commentary, however, the director strongly hints (but does not state definitively) that the muffins made by the Church contain some sort of drug that would cause the people who eat it to hallucinate demons. Karen is shown eating the muffins earlier, and the muffins were provided free to her psych ward patients. The only other people to definitively see demons in the film also had reason to have eaten the muffins (Betty, Sarah and Frankie all see demons and are church members; Neil at the very least hears the demons and he acknowledged that he was friends with Church-members and it is implied he may have been an ex Church-member himself). In this interpretation, the Church and its reverend were violent frauds who manipulated its members into acts of unspeakable horror.
Thanks Evan B!