The aliens are unstoppable. Humanity is screwed. Even after one of the large ships is blown to smithereens by a nuclear warhead, it begins to reassemble itself. After multiple failed attempts at getting out of the city and seeing members of their group picked off one by one, Jarrod and his pregnant girlfriend Elaine have given up on escaping. At the end of the movie, Jarrod and Elaine cling to each other as they are lifted into one of the alien ships and we see what happens to the abducted humans.
The aliens are harvesting human brains and plugging the brains into new alien bodies.
Elaine wakes up among piles of humans and begins crawling around looking for Jarrod as other people around her are picked up by alien tentacles and decapitated. The brains glow the same blue as the light that drew everyone outside to be taken. Elaine finds Jarrod just as he is picked up and his brain removed, but his brain is glowing red.
Earlier in the film, Jarrod was exposed to the blue light but was prevented from going to it by his friends. He recovers from the trance, but still shows evidence that he is being affected by it, so he must have been changed by it in some way.
When Jarrod's brain is plugged into the alien body, his conciousness is still intact. He goes to Elaine and she recoils. Alien Jarrod puts his hand across her pregnant bellly and touches her face the way he did in telling her he loves her and Elaine realizes that it is Jarrod.
Elaine is about to be picked up for harvesting, but Jarrod comes to her defense and fights off the tentacle.
The film ends with Alien Jarrod standing in defiance as other tentacles approach.