20 years after defeating the aliens who invaded the Earth, the world is almost a Utopia wherein technology taken from the aliens have made the planet a paradise. They built a base on the moon. And just as the anniversary is approaching, strange things are happening. President Whitmore who led the attack on the aliens 20 years ago is acting strangely and is drawing some strange symbols. David Levinson the man who figured out how to defeat the aliens travels to Africa to inspect one of the alien ships that crashed. The leader who is on possession of the craft, takes Levinson and they discover they sent a distress signal before it went down and apparently it was drilling through the Earth's core. The leader is also drawing the same things that Whitmore is. At Area 51, Dr. Okun who fell into a coma 20 years after being attacked telepathically by an alien wakes up and starts drawing the same thing Whitmore is. Whitmore tries to warn everyone that the aliens are returning. And sure enough a space craft appears just near the moon. The ship is different from the aliens'. The President is being advised to shoot it down but Levinson doesn't think they should. The President gives the order and shoots it down. Levinson wants to go to the moon but the President wants him to attend the anniversary celebration. Levinson asks Whitmore's daughter to ask her boyfriend who is among the ones at the moon base to pick him up. They go to the moon and he inspects the craft and finds something. He takes it and brings it to Area 51. At the same time an alien ship like the one who attacked the planet 20 years ago shows up and attacks the planet. Levinson arrives at Area 51 and gives the thing to Okun. Whitmore arrives and along with Okun and the African, they compare notes and they deduce why the aliens came to Earth 20 years ago. And now they are back to finish the job.