It's sometime in the 1920s and we see a snowstorm on a mountaintop in India. A man is sitting alone in a tent when he hears something. He goes out in the blizzard and climbs a peak to find a glowing blue-white sphere. He reaches out to touch it when everything goes white. The next morning, he wakes up lying in the snow. The sphere is gone, and there's a hole in his right glove with a small scar on the back of the hand.
Present day - Dr. Helen Benson (Jennifer Connelly) is an astrobiologist who's teaching a class. She goes home to her stepson Jacob (Jaden Smith). Helen tries hard, but Jacob doesn't seem to consider her to be his mother and he calls her "Helen." While Helen is making dinner, she gets a phone call. A man's voice refuses to identify himself or the situation and says someone will be there shortly to escort her somewhere. Right then, a bunch of government officials and cops show up and insist that she go with them. Jacob is sent to a neighbor's house.
Nobody will tell Helen what's going on and one official admits that he doesn't know either. She's taken to a military facility where the government has already assembled a large group of scientists, none of whom knowing why they're there. They're finally briefed on the situation - an unidentified object is coming to Earth at an unreal speed. They don't know what it is, but it's obviously aimed straight for Earth and will hit Manhattan. The scientists ask how much time they have and whether they can evacuate. They can't; it will hit in 78 minutes. Helen, who secretly snuck her cell phone in with her, calls Jacob to tell him that she just had to talk to some people about a big storm that night. She tells him she loves him very much and tries to talk with him longer, but he says they're having dinner and hangs up.
The scientists and soldiers are in the air in aircrafts, waiting for the impact. However, they count down and nothing happens. The object is slowing down as it approaches Earth and lands in Central Park (rather than smashing into it). The scientists and soldiers are wearing protective suits and they approach the object. It's a sphere just like the one in the beginning on the mountain, but it's enormous. Tons of soldiers and police show up to the park, armed and ready to fight. A figure walks out of the sphere and Helen walks up to it, even though everybody is screaming at her to stay back. Just when Helen and the alien (who looks like a large, man-sized, gray blob) are about to shake hands, someone shoots the alien. That's when a giant robot comes out of the sphere, charges up (eyes turn red), and emits a terrible sound that has everybody in agony. It then somehow shuts down everything in the park - lights, cars, and guns. After a moment, the robot turns everything back on and powers down (eyes go dark). Now everybody swarms to the alien, who's on the ground bleeding.
They take the alien to a military medical facility, but are unsure of what to do. They figure they better get the bullet out and call a surgeon. As the surgeon is extracting the bullet, he realizes the gray matter is falling away, revealing a pale, bald human body underneath. Within hours, the alien has fully formed and is conscious. Apparently, he can talk and says his name is Klaatu (Keanu Reeves). The U.S. Secretary of Defense (Kathy Bates) shows up and wants to interrogate (and perhaps torture) Klaatu into revealing his plans. She sees his presence at an act of hostile invasion. Klaatu says he has come for a purpose and has taken on human form. He asks to speak to the world leaders at the U.N., but she refuses. Klaatu says he is there is save Earth. Helen believes that Klaatu is not there to hurt them and helps him to escape. She injects him with saline solution instead of the drug the government prepared, and whispers to Klaatu to run away. Klaatu uses his powers (not exactly clear what they are, but he controls machines and people) to escape.
Meanwhile, more spheres have arrived all over Earth. They're smaller and about the size of the first sphere. The government is keeping Klaatu a secret and tries to find him by alerting the media and law enforcement and calling him an escaped convict. Klaatu is at a train station, but the entire world is in a panic over the alien invasion and all trains are delayed. He suddenly collapses when the stitches from his bullet wound and surgery. Helen later gets a call from the station, which says that her patient is there. She goes to find him and he uses the sample of the gray matter she kept on his wound, and it heals by itself. They are now driving away from the city with Jacob, who doesn't know who Klaatu really is. He says the government should kill the aliens, even if they're not evil, just in case. He says that's what his dad would have done.
Klaatu instructs Helen where to drive and for some reason, they end up at a McDonald's. Jacob gets out first to use the bathroom and Helen and Klaatu talk in the car. She tells him that Jacob's mother died when he was a baby and Helen married his father. Jacob's father had been in the army, but as a civil engineer, not a fighter. He had gone overseas to try to help rebuild. He died a year ago and Jacob still insists that he's been left alone.
It turns out Klaatu is meeting a friend - another fellow alien names Mr. Wu (James Hong) who was sent to Earth 70 years ago to learn about humans. He tells Klaatu that there is no hope for them. Humans are destructive and even they sense their impending doom. Klaatu says he will begin the process. Wu agrees it's the right thing to do, but says he will stay on Earth. Klaatu is surprised and says Wu will die if he doesn't leave. Wu says he doesn't care - he has come to love Earth and sees another side to humans.
Klaatu now instructs Helen to drive them to the middle of a forest, where he walks off into the trees. Helen tells Jacob to stay in the car and follow him. He is standing by a lake with one of the smaller spheres floating in the middle. All around them, all kinds of animals (insects, reptiles, fish) are flocking to the sphere. Helen returns to the car and Jacob realizes Klaatu is an alien. He gets angry, saying Helen shouldn't be helping "one of them." Klaatu returns to the car and Helen demands to know what he's going to do. He says humans are destroying themselves and the Earth and that "they" (assume the other intelligent life forms in the universe) cannot allow that. There aren't many planets able to sustain life so Earth is necessary. Helen understandably freaks out and pleads with Klaatu, saying that people can change. Klaatu refuses and says it's not in their nature to change. He tried to reason with them, but they wouldn't talk to him. Helen says the U.S. military and the Secretary of Defense do not represent Earth and that she will take him to talk to the leaders. Just then, a cop happens to pull up behind them and recognizes Klaatu as the escaped convict. When he tries to arrest Klaatu, Klaatu moves Helen's car with one hand and smashes the cop between it and the cop's car. Jacob starts screaming at Klaatu for killing him, but Klaatu takes some of the healing gray matter and puts it in the cop's mouth. He then touches the cop and brings him back to life.
Klaatu gives Helen a chance by going with her to see her friend, Professor Barnhardt (John Cleese). The Professor tries to reason with Klaatu, saying that all civilizations only change when they're at the precipice of a crisis. He says human will change, now that they are really at the edge of destruction. Meanwhile, Jacob is in the other room watching TV and sees a news bulletin about Klaatu. He calls the number to report him. Soldiers quickly show up at Barnhardt's house and Klaatu, Helen, and Jacob run away into the woods. However, Jacob quickly runs off on his own and Helen chases him. Jacob is yelling to the soldiers in helicopters so that they can be captured. He still insists that Helen shouldn't be helping Klaatu and that his dad would have killed him. Helen loses it and yells that Jacob's dad isn't there anymore. Just then, a soldier rappels out of the aircraft and grabs Helen. Before they can get Jacob, Klaatu shows up and destroys the helicopters (the ones without Helen inside) with his powers. Jacob runs away, afraid that Klaatu will hurt him, but Jacob almost falls off a small wooden bridge and Klaatu saves him. Jacob seems to finally warm up a little and asks Klaatu to help him get home. Klaatu agrees.
Meanwhile, the smaller spheres have all left Earth, carrying samples of live animals inside. The Secretary of Defense realizes the spheres were miniature Noah's Arks and that the people have been left to be wiped out. Also, the giant robot that emerged from the sphere with Klaatu is still in Central Park. The government has tried attacking it, but it destroys everything. They finally realize that the robot activates when there are acts of aggression around him. The government then quietly sneaks up around it with a huge casing and quietly seals it up, all without any hostility or gunfire. They take it to a remote military facility in a desert somewhere. They tried a diamond drill, but it broke, so they send someone inside next to the robot to fix it. However, a close-up of the broken drill reveals tiny robotic insects that are multiplying and eating away at the metal. They start spreading over and eating up everything, including the guy. The military officials watching through the glass incinerate the entire room, but the robot is unscathed. The bugs keep eating away everything, including the glass. Turns out the robot is actually made up of the tiny insects and he dissolves himself into a black cloud of flying insects, escaping the facility, destroying all the soldiers and weapons outside, and flying over the rest of the world and eating up everything.
Helen has been imprisoned but she keeps asking for the chance to change Klaatu's mind. The Secretary of Defense sees that it's hopeless and their only chance is Helen. Helen and her friend Michael (Jon Hamm) go to find Klaatu and Jacob. Jacob calls Helen and agrees to meet somewhere. It turns out it's the cemetery where Jacob's father is buried. Jacob wants Klaatu to bring his father back to life, but Klaatu says there are things even he can't do and seems sincerely sorry. Jacob breaks down in front of the grave. Then Helen shows up and tells Jacob that he's not alone and his father is not gone - she sees his father in Jacob every day. Jacob finally apologizes to Helen and they hug. Klaatu is watching them and says he understand now. He sees there is another side to humans and agrees to try to stop the destruction process.
The black clouds of robotic insects are sweeping over big cities, destroying everything. Michael, Helen, Klaatu, and Jacob are driving back to Manhattan because Klaatu must get back to the sphere. The city is deserted, but soldiers are still waiting at checkpoints to look for Klaatu. They drive through a military checkpoint because there's no time to stop. At first, the soldiers chase them, but then get orders to let them go through. The group gets to the park, but senses something is wrong because there is nobody near the sphere. All the cops and soldiers have left and the park is empty. They drive straight toward the sphere, but it turns out the park has been rigged with land mines to kill Klaatu. The car flips repeatedly and hits a tree, but only Michael dies and the other three are okay. They have to run to the sphere, but the black cloud is there by now. They take refuge under a bridge, but Jacob starts bleeding from his nose and mouth and collapses. Klaatu says the bugs are inside him, killing him. Helen's nose starts bleeding too. Helen pleads with Klaatu to save Jacob. Klaatu takes both their hands and all of the bugs leave their bodies and enter Klaatu's. Klaatu then runs out into the black cloud to get to the sphere. His clothes and skin are gradually being eaten away and he starts to fall. He manages to touch the sphere, and as soon as he does, everything goes white. The bugs all deactivate and die, falling to the ground like silver sand. The sphere and Klaatu have disappeared. Then EVERYTHING shuts down - lights, buildings, cars, etc. People everywhere cautiously emerge. Helen and Jacob walk out from under the bridge.
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