Jim awakens one morning to find that his cranium has more than doubled in proportion. Initially embarrassed, it takes Jim nearly a week to leave his apartment, and his first stop is a head specialist. But good Dr. Axel can offer no solid answers, so an irritated Jim heads out the door for home. On his way, he's cornered by a gang of thugs, who have absolutely no idea what's awaiting them. Jim's head splits in two and out jumps a little purple alien who attacks them. After beating up the aggressors, the alien pops back into Jim's head, which seals up behind him. Dumbfounded, Jim heads home and interrogates the alien. Turns out his name's Roy, and he's on a mission to save the Earth from a parasitic alien named Gork. Dr. Lucas Elliott, a disgruntled FBI agent, catches the thugs telling their story on Eye Witness News, and begins his pursuit of Jim.
Jim had forgotten that he had set up a date with Madelyn, which Roy encourages him to keep.
Jim awakens to find that Madelyn has been possessed by Gork. Roy explains that the Gork race has made plans to invade the heads of Earthlings, and he came to Earth with a machine that could stop the invasion -- but it was broken into five pieces and scattered across the planet. Meanwhile, Dr. Elliott bursts in with his cronies to interrogate Dr. Axel. He tells of his childhood encounter with a Gork, then proceeds to kidnap the head specialist.
Roy spies the first piece of the anti-invasion machine lodged in the face of the Statue of Liberty. Roy hops on the Staten Island Ferry to retrieve the piece, but he finds himself hunted by sightseers who think he's an alien California Raisin. Meanwhile, Jim goes to a meeting of ""human anomalies"" and befriends the group -- but Jim and Roy's telekinetic link cuts their meeting short when Jim receives a cry for help. Jim enlists the anomalies' aid to help him save Roy from the angry mob.
Dr Elliott continues to interrogate the kidnapped Dr. Axel, but his session is cut short when he gets a call to examine an unusual meteor that just came into the museum. Meanwhile, Jim gets a phone call from Madelyn, who wants to see him. They have a brief meeting, which climaxes when the Gork wakes up and regains control of his host. Jim and Roy then head to the museum to regain the ""meteor,"" which is actually holds a gemstone which is a piece of the anti-invasion machine -- but it leads to an encounter with the inept FBI agents and the Gork. The Gork uses the meteor's stone to immobilize Roy.
Roy is dying, so Jim gathers the anomalies and the group hatches a plan to rescue the kidnapped Dr. Axel. But shortly after escaping, Jim has Dr. Axel return to meet Dr. Elliott, claiming that Elliott's outlandish childhood memory has merit. Meanwhile, Jim pays Madelyn a visit, knowing that he's being followed by the FBI.
Roy uses his telepathic abilities to find the next piece of the anti-invasion machine. He locates it in a jungle. So Madelyn, Jim and Roy are off to the forest, where their plane goes down and they're pursued by headhunters. Meanwhile, Gork convinces Dr. Elliott that the machine he has is to locate the other alien race's weapons.
Jim and Roy are off to the small town of Shallow Ditch to recover another piece of the anti-invasion machine, as Elliott's FBI cronies are searching the sea for the black orb, the last piece. Jim finds himself playing King Arthur as he tries to pull the key (shaped like a sword) from a stone.
After a near-death experience whilst trying to get the orb, Elliott's henchmen blow him off and head to a cabin by the lake with the orb. Elliot becomes infuriated and Gork becomes increasingly deceptive. Roy discovers the location of the orb, so he and Jim set out to get it -- then wind up nearly getting blown up in the cabin by the lake.
Jim and Roy hide the orb, but Dr. Elliott has his sights set on finding it. So when they reveal to the group that ""Einstein knows where it is,"" Elliott's spy leads him to it. Meanwhile, Roy finds a mutual attraction with Mona, so he spends a romantic evening at her house, where he learns that she has a tail... and that she's Elliott's spy. The evening ends with Elliott busting in and taking Roy prisoner.
Now that Roy's been captured, Jim's skull has returned back to normal size, but his equilibrium is out of whack. So Jim pays a visit to Dr. Axel, who offsets the equilibrium damage by strapping an anvil to Jim's head. Meanwhile, Mona arrives declaring that she's in love with Roy, and she wants to help him escape from Elliott's evil clutches. So the anomalies and Dr. Axel set off to break Roy out of the FBI building. Meanwhile, Gork tries to convince Dr. Elliott that he's the good alien and Roy is the parasitic alien.
As the anomalies prepare to rescue Roy, the Gork race prepares their invasion. But as Jim and the gang enter the compound, Gork escapes with the orb inside Dr. Elliott's head. Meanwhile, Ray learns that the lawnmower blade that's embedded in his skull wasn't an isolated case.
Dr. Elliott finds that the tables have turned â€“ he's now the captive strapped to a table. Jim and his friends try to develop the anti-invasion machine without the orb, and soon find that they're running out of time as the Earth is bombarded with Gorks. At the last minute, they get the machine working and thwart the attempts of the parasitic race to take over the world.