Will is cruising through Manhatten when he spies the mannequins outside the DVD store. Confused and overcome with emotion he gets out the car and walks towards 'Fred' - and as he does so trips a device based on his own booby trap that hoists him from the ground and leaves him unconscious.
Sam is frantically trying to get her master's attention as the sun starts to go down. Robert wakes in time and desperately tries to work himself free of the trap. Meanwhile the infected Alpha Male is waiting with some hounds from hell by his side.
As soon as the sun has set sufficiently, the dogs race towards Robert -- Sam fights them off, but is bitten badly. Robert makes it back to the car. Back at his lab he injects Sam, but she is too far gone through the transformation and he has no choice but to break her neck when she starts to bite ferociously.
Sick of living and looking for revenge, he gets into the car and drives down to the pier. The infected people run and leap towards him - he just bats them down with his car, and then turns it into an I-Robot style carousel as they spin around and fly off. The car crashes spectacularly and Robert is resigned to death - he sees the white light as he slips into unconsciousness.
He wakes in his bed to hear Donkey from Shrek. Unsure if it is a dream he walks into the main room to find a young boy watching movies on his tv. His mother introduces herself as Anna, and that they heard his radio message while following a path north to Vermont - where she was told there was a survivors colony by God. Robert is moody and doesn't believe her.
As night falls Robert suddenly realises to his horror that Anna didn't take the usual precautions and so the infected zombies now know where they live. He locks up the house, but they soon break in through the roof.
They make it down to the basement and lock themselves behind a bullet-proof glass door. Robert realises that his antedote is working on the captured woman - he takes a syringe of her blood and gives it to Anna. He pushes Anna and the boy into a secret passage in the wall and closes it behind them.
The alpha-male zombie is irate. Robert tries to reason with him. As the zombies are about to break the glass, Robert ignites a grenade and they are all blown to pieces.
It cuts to a peaceful country road heading north, where Anna and her son have found a human survivors' colony behind large-scale perimeter gates, and where she'll hand the vaccine-syringe over for mass production.
(In the alternative ending, they are back in the lab and Robert realises that the alpha-male just wants his partner back. Robert unties her and helps her up. He gives her to the alpha-male, who summons his subordinates back, and they leave the room in peace. Robert then rides with Anna and the boy to the colony.)