Jigglypuff is walking through the forest, singing to himself as he walks. A Pidgey and Caterpie fall from a tree, asleep, and Jigglypuff scribbles all over their faces. Suddenly, a kettle falls on his head. He looks up, and sees a strange object fall from the sky. He runs over, and finds the smoking wreckage of a spaceship. A door opens, and several Clefairy jump out.
The next day, Ash, Misty, and Brock are indulging themselves in a little ice cream. Suddenly, a Clefairy shows up, but then runs off. Ash and his friends dash after him, leaving their stuff behind. When they return, the discover that someone has stolen their bags. They dash off to report it to Officer Jenny. Upon reaching there, however, they discover that there are several other people with missing items as well. Brock wonders aloud why anyone would steal these things, and a man shows up telling him the answer: Aliens. He introduces himself as a UFO tracker, and pulls out a scrapbook filled with pictures, newspaper clippings, and interviews that he says prove that aliens exist. Ash flips through, and a cook (who lost a pot) points to a picture of a spaceship, saying that he has seen it before. The scientist starts to shake him, and he says that he saw it about three nights ago, at the edge of the forest. Jenny tells them all that the reports of missing objects started three days ago, and they gasp.
A few minutes later, Ash and his friends follow the scientist, who has a tracker to find UFOs and aliens. Ash and his friends talk amongst themselves, and the tracker starts to go off. They all look up, and see a glowing object sink down and land in front of them. A hatch opens, and two aliens come out, grab Pikachu, and go back inside. The spaceship starts to take off, and Ash yells at the aliens to give him his Pikachu back. Inside the spaceship, the two "aliens" take off their masks, revealing themselves to be Team Rocket. Pikachu tries to shock them, but he's inside a glass jar which blocks the electricity. Ash and his friends look above the "UFO" and see a crane towing it upwards. Ash sends out Pidgeotto, who snaps the cable. The saucer falls and smashes apart, revealing Team Rocket inside. They say their motto, and another Clefairy shows up. The scientist's tracker goes off again, and he concludes that Clefairy is an alien. Jigglypuff walks up, and the tracker goes off again. Misty yells at the scientist, and the tracker goes off one more time, indicating that Misty is an alien. She knocks the scanner out of the scientists hand, it breaks, and he starts to sob. Meowth tells Jessie and James to grab Pikachu, but the Clefairy has already done this, and is hurrying off. Team Rocket dashes off, but hit an invisible wall, falling over. Jigglypuff dashes after the Clefairy, with Ash and his friends soon behind. Clefairy goes into an alley, and they all go in after him, only to not see him anywhere. Jigglypuff points to a manhole, and they open it up. Jigglypuff jumps in, and everyone follows.
They plummet for a while, and finally come out into a large underground cavern. They look around, and see a huge spaceship with several Clefairy working on it. They see some Clefairy holding different objects, and Brock concludes that they are the ones who were stealing it all. They see another Clefairy holding Pikachu (who is still in the jar) and carrying him onto the ship. Ash wonders what they would need Pikachu for, and the scientist tells him that he is probably going to be used to power the ship. A large panel drops down from the ceiling, and all the Clefairy rush inside. The scientist tells Ash that the ship is going to blast off soon, and he and Jigglypuff dash inside. Brock runs off to tell Officer Jenny, and Misty and the scientist follow Ash inside. Team Rocket, behind another rock, plot to hijack the ship, and take Pikachu and all the Clefairy to the boss. They also hurry on board.
Ash, Misty, and the scientist walk around the ship, looking for Pikachu. They find him in another room, and run inside. Several Clefairy jump out, however, and block the way. Ash begs the Clefairy to give Pikachu back, but they refuse. Jigglypuff approaches one, and pounds him. The Clefairy jumps up and pounds him right back. Jigglypuff approaches again, and knocks Clefairy up with a Doubleslap. The other Clefairy, angered, attack, but Jigglypuff Doubleslaps them all into submission. He then walks off through another doorway with the scientist soon behind. Ash pounds on the glass of the tube Pikachu is in, but to no avail.
Jigglypuff and the scientist discover the control room, with another Clefairy inside. Jigglypuff points to a joystick on the panel, and it turns out to be his microphone. Clefairy jumps out of the chair and Headbutts Jigglypuff. Jigglypuff jumps up, and Doubleslaps Clefairy. Clefairy and Jigglypuff start to Doubleslap each other, and the scientist sits down at the controls. He accidentally breaks the joystick, and Jigglypuff jumps on top of him, taking it. He then starts to sing, and the music is heard all through the ship, putting everyone to sleep. Jigglypuff stops, angrily scribbles all over the Clefairy's and the scientist's faces, and walks out.
The countdown ends, and a small mallet hits Pikachu. He gets angry and does an electric attack, powering the ship. The ship starts to move down a tunnel. Above ground, Brock is pleading with Officer Jenny to believe him about the spaceship, but it isn't working. A panel of the road removes itself, and the spaceship rolls out, shedding several objects. The rockets fire, and the spaceship rolls up a building and into the sky. Inside, Team Rocket prepares to try to bash through a door, when the part they are in separates from the ship and falls to the ground.
Pikachu's electric attack finally gets the best of the glass that surrounds him, and it shatters, waking Ash and Misty up. Ash happily picks Pikachu up and hugs him. Misty notices their backpacks sitting against the wall, and they pick them up. Sparks start to fly in the control room, and the ship starts to waver in its flight. Ash and Misty reach a door to the outside, but see that they are extremely high in the sky. The ship approaches a skyscraper, and Ash sends out Bulbasaur. He tells him to use his vines to grab onto the skyscraper and they all swing to safety. They watch as the spaceship flies off into the distance.
Later, somewhere in a forest near a campground, the ship crashes. Several people approach, and a hatch opens up. The scientist, dressed as an alien, comes out, and scares them all away. He falls over, the Clefairy dash out, and start to steal things from the people there. Meanwhile, Ash and his friends are thanked by the citizens and they walk towards Viridian City, with Jigglypuff soon behind.