Skyline

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Jarrod and his girlfriend Elaine have flown to Los Angeles for Jarrod's best friend Terry's birthday party. They celebrate with Terry's wife, Candice, and his assistant, Denise. During the party, one of Terry's employees, Ray, welcomes Jarrod to L.A., thinking he has moved there to join Terry's special effects company. During a private argument about whether or not they should move, Elaine reveals she is pregnant.
The next morning, blue lights descend from the sky, hypnotizing anyone who looks at them. The light affects them physically, causing them to become zombie-like. Any immobilized humans are collected by the light machines. Ray is taken, but Jarrod is saved when Terry tackles him, and he slowly returns to normal. He and Terry go to the apartment roof to investigate the lights. They see large alien spaceships descending through the clouds and vacuuming up thousands of screaming people. They are attacked by one of hundreds of flying alien drones and forced to retreat from the roof. As they attempt to open the door before the alien can get them, Elaine quickly opens it from the other side and accidentally looks directly into the aliens light. The alien hypnotizes Elaine with its blue light, but Jarrod and Terry are able to save her and close the door.
Back in the apartment, Jarrod believes the open water would be a safer place, since there are no machines over the sea. They attempt to reach the marina by car, splitting into two cars: Terry and Denise in the first, followed by everyone else in the other. They encounter a bickering couple, Colin and Jen, also getting ready to flee the building. As Terry's car exits the garage it is flattened by a massive two-legged alien. Denise is killed but Terry escapes. As he begins to run he is abducted. The others run back into the garage, where they encounter another alien lifeform in the shape of a large multi-tentacled squid that takes Colin. It corners the rest of the group before the building's concierge, Oliver, slams into it with an SUV. They find Colin is still alive inside the creature. As they try to free him, the squid creature comes back to life, sucking out Colin's brain and regaining its energy. As they run back into the building, Jen is abducted.
The next day, the United States Air Force launches an attack against the alien spaceships and flying alien drones using stealth unmanned combat aerial vehicles and conventional drone aircraft armed with air-to-air missiles (a "jet engine" powered MQ-9 Reaper). Only one stealth plane (an X-47B) gets through the carnage and just before it gets destroyed it fires a nuclear missile, hitting the mothership. The huge detonation blows the ship apart which crashes, but minutes later as the mushroom cloud clears, the alien ship rises back into the air and begins to slowly repair itself. After Jarrod tells Elaine that the alien light made him feel powerful, he is adamant that safety must be found outside. Oliver wants to stay inside and tries restraining him. Jarrod physically starts changing as he lifts Oliver off the floor and vows that he will protect his family.
Helicopters arrive, inserting squads of soldiers. Jarrod and Elaine go to the roof hoping to catch a ride to safety. Oliver and Candice stay in the penthouse, but are found. Candice is hypnotized by the blue light and is abducted; Oliver attempts to kill a tanker alien by turning on a gas stove and igniting a lighter, causing the room to explode. The soldiers are thrown off the roof by the aliens and a squid alien attacks Jarrod and Elaine. They kill it, but with Jarrod badly hurt. They are surrounded by the aliens, so resigned to their fate, they look into the blue light, embrace and are sucked up into the mother ship as it slowly flies over the building.
A brief montage shows that cities all over the world have been overrun by the aliens.
Inside the alien spacecraft, Elaine wakes up on a pile of human corpses. Tubes are sucking human brains into machines; probes go through the pile looking for what they can find. Elaine sees Jarrod in the pile but has to watch helplessly as his brain is removed. She is probed, but left alone since she is pregnant. Elaine is transported to another chamber where other pregnant women have been sent. Meanwhile, Jarrod's brain, glowing red instead of the usual aliens' blue, is inserted into a new alien body.
Animating the alien body, Jarrod seems to retain control, and comes to the aid of Elaine and their unborn child. He destroys the machine that is probably trying to extract the fetus. Elaine recognizes him when he caresses her belly and her head. He then turns around to confront advancing aliens, and in between the credits, a series of still images depict "Jarrod" protecting Elaine and their child from the other aliens.

Question: Where does the Nuclear missile hit?
Answer: Mothership