In 1928, on an expedition in the snowy Karakoram mountains of India, a mountaineer (Keanu Reeves) encounters a glowing sphere of ice. After breaking away a chunk of ice with his pickaxe, he is blinded by a fierce & ferocious light, then finds himself waking after a sudden loss of consciousness, with the sphere now gone and a scar on his hand.
Fast forward to the present day. A famed astrobiologist at Princeton University, Professor Helen Benson (Jennifer Connelly) goes home to make dinner for her stepson Jacob (Jaden Smith) when she receives an odd phone call that "they" are on their way to pick her up. When asked who "they" are, the United States government pulls in front of her house and hastily tell her she is under Federal protection and must leave with them immediately. They arrive at Ft. Linwood in New Jersey where she is assembled with others in a conference room and is shown that a large unknown object with a speed of approximately one-tenth the speed of light is due to impact Manhattan in approximately 78 minutes. She is put on a helicopter along with a group of other scientists to formulate a survival plan. Just as they brace themselves for impact all is quiet. Apparently it has slowed down and is not going to crash. Dr. Benson turns around to look out the window on the helicopter just in time to see a large bright sphere approach the ground.
It is a spaceship and it lands very gently in Central Park. A being named Klaatu (Keanu Reeves) emerges from the sphere, around which the military has established a perimeter. Just as Dr. Benson is about to shake hands with the being, it is shot. A gigantic robot emerges, emitting a sound that paralyzes humans and disrupts all electrical systems in New York City. Before the robot can take the being back, it is orderded to shut down by the being. The being is gathered up by the military and rushed to the military hospital where the doctors revive the dying being. A surgeon is brought in to remove the bullet. While attempting to remove the bullet he notices that the being's outer layer is a jelly substance much like whale blubber and it begins to fall off on its own. The theory of this was is that it is the being's "placenta" much like a human baby and that it was "born" here on earth. In 1928 when it landed the first time, the patch of skin removed from the mountaineer's hand was a DNA sample so the being could replicate itself into human form. The being is immediately put into an incubator while it "grows". Time passes and we see a full grown "human" inside the incubator. Once fully grown and awake he begins to thrash around in the incubator and the first person there to speak to him is Dr. Benson.
While recovering he is interviewed by Regina Jackson (Kathy Bates), the United States Secretary of Defense, Dr. Michael Granier (Jon Hamm) and Dr. Benson. He introduces himself as Klaatu. He informs them that he is a representative of a group of alien races sent to talk to the world leaders. Jackson laughs at this and tells him that she is the nearest he is going to get to their president and to just tell her what he wants. He refuses so she orders Klaatu instead be sent to a secure location, drugged and interrogated. Dr. Benson volunteers to do the honors of drugging him but instead injects him with a solution of saline while whispering to him "run". During the polygraph Klaatu manages to take mind control of the interrogater and escapes. He makes it as far as a train station when his bullet wound opens and he needs Dr. Benson's help. Dr. Benson is at home with Jacob when she gets the call from the train station that Klaatu is there asking for her and she rushes over there with Jacob in the back seat. After leaving the train station they are pursued by the authorities throughout Newark, New Jersey, and the forested Highlands.
The presence of the sphere has caused a worldwide panic. The United States military manages to capture the robot from the beginning whose name is "GORT" (Genetically Organized Robotic Technology) after it thwarts their attempts to destroy the sphere using unmanned aerial vehicles that launch Hellfire missiles.
At a McDonald's, Klaatu meets with a Mr. Wu. We learn that he is another alien who had been assigned by the same group of alien civilizations to live with the humans for 70 years. Upon learning from him of humanity's destructive tendencies, Klaatu decides that humans shall be exterminated to ensure that the planet with its rare ability to sustain complex life can survive. Mr. Wu decides to stay on Earth, having seen another side to humanity that he loves. Klaatu can't see this love so he orders smaller spheres previously hidden on Earth to begin taking animal species off the planet. This is compared to Noah and his ark and the flood that destroys the world.
Meanwhile the robot, is subjected to experiments in an underground facility in Virginia. It then transforms itself into a swarm of insect-like nanites that begin destroying everything in their path back to Manhattan, including an armored battalion of the U.S. Army.
Dr. Benson tries to convince Klaatu that the world is not bad and that humans can change the earth for the better. Still unconvinced she then takes him to the home of Nobel Prize-winning Professor Barnhardt (John Cleese), where they discuss how Klaatu's own species went through a drastic evolution to survive its own star's demise. Klaatu is convinced by Helen and Jacob that humans can change their ways and are worth saving. However instead of quietly sleeping in the next room, Jacob calls a 800 hotline and reports where Klaatu is. He quickly learns his mistake when Dr. Benson is captured by military personnel and he is left alone with Klaatu. The two of them keep heading towards the sphere. Meanwhile, Regina Jackson realizes that convincing the alien to change its mind might be the only way to ensure the survival of humanity. Helen is allowed to leave and together with Dr. Michael Granier they rendezvous with Jacob and Klaatu at a cemetery.
At the cemetery, Jacob leads Klaatu to the place where his father is buried. Jacob begs Klaatu to use his powers and bring his father back to life. Klaatu is unable to do this. He consoles Jacob by explaining how no one ever truly dies because the universe has a use for everything. Everything is just transformed into something else. At this moment, Helen and Michael arrive. Helen tells Jacob how much she missed his father and they share a good cry. The scene between the two convinces Klaatu to save humanity. Klaatu recognizes the other side that Mr. Wu loves about humans.
Klaatu says he will try to stop it and they head towards the sphere. Dr. Benson notices something is odd the way the entire town has been evacuated and how when after driving through a road block they are not chased by the military vehicles. As they approach the sphere, she yells for Michael to stop the car. Just then, a targeted missile strike authorized by the president hits the sphere. It blasts the car into a tree and kills Michael. Just then the nanobot cloud arrives. Klaatu warns that even if he manages to stop GORT, there will be a price to the human way of life. There is not enough time to make it to the sphere so they run towards a footbridge to hide under. But inside Jacob and Dr. Benson have bloody noses and it is revealed that they have been infected by the nanites and are already starting to die. She pleads with Klaatu to save Jacob. Klaatu saves both of them by transferring the infection to his own body, then sacrifices himself to stop GORT by walking through the nanites to the sphere and touching it. His actions cause the sphere to emit a massive EMP which destroys GORT, saving humanity, but at the price of Earths technology becoming useless and immobile. As the sphere is leaving, Jacob realizes that Klaatu didn't die. He just merged into the giant sphere. The spheres surrounding earth leave with the giant sphere.