Michael arrives and arms the patrons as the entire sky plunges into blackness. Hundreds of cars approach, filled with possessed people who begin to attack the diner. Michael leads the patrons in the fight, but Howard is dragged away. Later, Michael explains that God has lost faith in mankind and has sent His angels to destroy the human race. He also reveals that Charlie's baby must stay alive, as it is destined to be the savior of mankind; Michael disobeyed God's order to kill Charlie's baby, as he still has faith in humanity. The next morning, Sandra discovers Howard crucified behind the restaurant and covered with huge boils. She tries to rescue him, but he violently explodes into acid. Percy dies shielding Sandra from the blast, and Sandra is driven insane. Meanwhile, the remaining survivors hear a radio transmission that reveals there are other pockets of resistance. One such refuge is nearby, but Michael advises them not to go, since they would be too vulnerable on the move.
That night, a second wave of possessed attack. Kyle is lured out by a trap and killed, and the attack pushes a panicked Charlie into labor. Audrey and Michael help her deliver the baby as trumpets sound, signaling the approach of the Archangel Gabriel. In a panic, Sandra breaks her restraints and tries to give the baby to the possessed, but Michael guns her down. Moments later, Gabriel enters the diner and seriously injures Bob. Michael urges the group to escape and enigmatically tells Jeep to "find the prophets, learn to read the instructions". The hordes of possessed humans are unable to approach Charlie's baby, so Jeep, Audrey, Charlie, and the baby make their way to Michael's cruiser. Gabriel and Michael fight to a standstill, ending with Gabriel's stabbing Michael through the chest with his mace. Michael dies and his body disappears. Dying, Bob uses a lighter engraved "hope" to ignite the diner's gas main and blow up the diner, incinerating himself and the remaining possessed.
Jeep's body is covered in the same mysterious drawings seen on Michael's body; Jeep concludes that the tattoos are his instructions. Gabriel then appears and swoops down on the fleeing car. As he tries to reach Charlie, Audrey jumps on him and sacrifices herself by yelling at Jeep to slam on the brakes, sending her and Gabriel through the front windshield as the car crashes. Gabriel finally corners the three in the nearby mountains. He is about to kill them when Michael descends from Heaven, an angel once more, and stops Gabriel. Michael tells Gabriel that Gabriel gave God what he asked for but Michael did what God needed, thus giving humanity another chance; Michael also gives the impression that everything that happened so far was part of God's plan to test His angels. Ashamed, Gabriel leaves. Michael explains to Jeep that he is the child's true protector and to have faith they will see him again. Michael then flies off. Charlie and Jeep make it to the top of the mountain and see a small town in the valley below. Sometime later, Charlie, Jeep, and the baby are seen driving off into the distance with a station wagon full of weapons.