Americans Ben and Sean (Max Minghella and Emile Hirsch) travel to Moscow to sell their social networking/party locating software. As they approach the airport, their plane short circuits due to an electrical storm but regains power. After arriving, they find their Swedish business partner, Skyler (Joel Kinnaman), has betrayed them and already made a deal with the Russians, using a knockoff application. They go to a nightclub and meet Natalie (Olivia Thirlby), an American, and her Australian friend Anne (Rachael Taylor). The lights go out in the club and everyone heads outside. There, they witness what appears to be an aurora. Balls of light fall from the sky and then fade away. When a policeman investigates he is disintegrated. The invisible entities begin hunting and disintegrating people, sending them into a panic.
Ben, Sean, Natalie, Anne, and now Skyler hide in the club’s storeroom for seven days. With most of their food gone, the group plans to go to the American Embassy. They find the city full of scorched cars and cinders, but empty of people, except for a wary old woman who warns them of “the ghosts”. Ben and Sean search for supplies in a police car near Red Square while the others hide in the nearby GUM department store shopping mall. While they are searching the car, a barking dog discovers and confronts an alien, but is disintegrated. Ben and Sean successfully hide under the car as the alien moves closer, causing the car’s lights and siren to turn on. The alien moves on and the men run to the mall. Sean realizes that light bulbs and other technologies give the aliens away. The group takes shelter in one of the mall stores. Sean and Natalie go to look for clothes and almost run into an alien who can’t see them through a glass wall. Sean theorises that the aliens can only see their electrical charge, but not through glass or other insulators.
The group finds the American Embassy gutted and lifeless. All except Skyler go to the roof to get an aerial view. They find a logbook telling them that the invasion is worldwide. They also find a radio broadcasting a message in Russian, and hear gunfire. Ben and Sean go outside to help Skylar, but he is killed. The others see a light in a nearby apartment tower and go to investigate, bringing the radio they found. They find a young woman named Vika and a man named Sergei, an electrical engineer. Sergei has made his apartment into a giant Faraday cage that hides everyone from the aliens. He has also developed a microwave gun that weakens an alien’s force field, so that it can actually be seen and killed. Vika and Sergei translate the message, which says that a nuclear submarine K-152 Nerpa is waiting in the Moscow River to take survivors to safety.
As Sergei shows the men the microwave device, Vika, Natalie, and Anne go to other apartments to gather supplies for the submarine journey. An alien senses them outside the Faraday cage and gives chase; Anne hesitates following Vika and goes another way, causing Natalie to follow her back inside. When they get to the apartment, Natalie is unable to close the door and the alien gets inside. Sergei shoots the alien with his gun and finds that it is only stunned. The alien disintegrates Sergei while the others get out by the fire escape. Anne hesitates again and is disintegrated while trying to escape. Natalie sets the apartment on fire as they climb down and meet up with Vika.
They meet up with a Russian police team with improvised armor led by Boris who manage to wound an alien with conventional weapons. Sean collects a piece of the alien’s body. The small police band were also able to build another Faraday cage at the Russian State Library. Boris and his men eventually agree to help the remaining four to get to the submarine. The policemen believe that the aliens are strip mining for conductive metals since giant light columns can be seen drilling all over Moscow. As they move through the subway, an alien discovers them and they escape on the tracks. Vika hides behind a pillar, unable to join the others without being seen. Ben helps her climb down to the tracks, but gets disintegrated.
The survivors make it to a powerless patrol boat on the river and drift downstream to the waiting submarine. The boat nears the submarine but runs aground. As they attempt to push free, a new light beam destroys a large apartment building right next to the river, causing the boat to capsize. Sean and the policemen swims towards the submarine but upon reaching it discover Natalie is missing. They see a flare fired from Natalie’s flare gun in a railway and bus yard near the river. Sean is determined to get her, possibly missing his chance to escape. The policemen agree to help him rescue her. The Russian submarine crew, after expressing doubt about the rescue, assist by building another microwave gun with stronger batteries.
After the team manages to destroy an alien, Sean finds Natalie on a bus while the policemen and Vika destroy three more aliens using the microwave guns and water. As Sean is about to get off the bus with Natalie, an alien climbs on board, locks the door, and sends the bus speeding around the bus yard. It grabs onto Natalie’s leg, but Sean blasts the alien’s shield with the microwave gun. He then discovers the alien’s weakness when he throws a piece of the wounded alien he had collected earlier, and it destroys the unshielded alien. The two stop the bus and narrowly avoid a collision.
After returning to the submarine, the police team decides to stay and fight for the city, and Boris tells them that now the war has begun. Sean, Natalie, and Vika plan to spread what they learned about the aliens – the microwave guns and their vulnerability to pieces of other dead aliens – to the rest of the world. Sean and Natalie, the only survivors of the original group along with Vika, nearly share a kiss on the submarine. In a pre-credit scene, as the submarine cruises through the Caspian Sea, they learn that survivors in Paris managed to destroy an alien mining tower.