Thanks to a generous cash bonus given to Team Rocket for their excellent salesmanship at the Twinleaf Festival, the group has constructed a state-of-the-art secret base, which they use to fool Ash and his friends into thinking is a Pokémon Trainer’s center. But both Team Rocket and our heroes soon discover that the base contains a mischievous Togepi that delights in playing prank after prank. Disguising herself as a sweet Togepi, she fools everyone time and time again. Finally, using Attract, Togepi puts Pikachu, Croagunk, and Meowth under her spell, forcing them to pilot Team Rocket’s base, which turns out to be a real rocket ship, to the farthermost reaches of the universe!
Our heroes and Team Rocket join forces and come to the rescue, only to find themselves all sent into outer space! Panic ensues as the rocket ship begins to lose control and plunge back down to Earth. Just when things are looking hopeless, Togepi decides that she’s had enough fun for one day. She saves the ship and leaves the Team Rocket members trapped in their own cell. Meanwhile, our heroes are a bit frazzled, but they begin looking forward to Lilypad Town and Dawn’s next Pokémon Contest. Ash, always looking at the bright side, even marvels at the fun of being in outer space!
Ash and his friends come across a tall tower. A disguised Team Rocket surprises them and mentions that it is a Trainer Tower, pushing them inside, leading them right into a pit trap that sends them into a cell. When they recover, Team Rocket appears without disguise on a video screen. Team Rocket head up towards the tower, not realizing that a Togepi has sneaked on board. While Togepi are normally known for being cute and kind, this one has an evil grin on its face suggesting that it doesn't plan on helping out at all.
Up in the tower, Team Rocket celebrates since their work at the Twinleaf Festival was able to pay for such an expense. The Togepi waddles into one of their food storage closets, making a lot of noise. When Team Rocket heads out to check it, they find the food bank left in empty chaos. They hear another rattle at another food bank, where they catch Togepi. It tosses a banana peel at Meowth, angering it to attack, but it quickly moves away. Togepi lands on the other side of the room, and as they prepare to attack, Togepi cries and tells Meowth that it is a different Togepi, that an evil one is still loose having used Teleport to get away. It convinces Team Rocket as they search for the other Togepi, but the manipulative Spike Ball Pokémon slips away.
Meanwhile, Ash and his friends try to break out with Pikachu, Piplup and Croagunk's attacks, but the bars are too resilient. Togepi appears from the elevator directly across from the cell and Dawn, having never seen a Togepi before, checks it with her Pokédex. They try to tell Togepi to get away, but it helps by triggering a lever, raising the cell bars. They enter the elevator and head up to the fifth floor, but as they exit, they fall into another pit trap, Togepi watching and laughing. They wind up back in the cell. Also, Team Rocket continues to find ransacked food banks, as they wonder if their rooms have been hit too. James finds his bottlecaps intact, but Togepi uses Psychic to make him chase it. It proceeds to affect Jessie and Meowth as well, using its Psychic powers to send Jessie's dresses into a mud bath while affecting the Giovanni petting robot Meowth has, making it rub so hard that the friction sets Meowth's fur on fire.
Back at the cell, Togepi once again releases Ash and his friends and takes them into the elevator. They head up to the rooftop, where once again they fall into a pit trap and wind up back in the cell. Dawn suspects that Togepi is deliberately doing it since it never fell into the pit trap as well. Togepi appears crying, trying to apologize, which successfully tricks Ash and his friends. It lets them out once again, but instead of running to the elevator, they stay on the current floor. However, they once again hit a pit trap and wind up back in the cell, which solidifies the suspicion that Togepi is behind it.
Meanwhile, Team Rocket meets back up as they realize that Togepi is evil too. The elevator nearby appears as Togepi taunts them. They try to attack, but Togepi roasts them with Flamethrower. They try to run forward, but they hit a pit trap and wind up in the cell with Ash and his friends. They all realize that Togepi has been playing them all and is in control. It appears by the elevator, prompting Jessie to have Yanmega fire SonicBoom, but it seems to disappear, a decoy taking the hit. Togepi reappears, seeming gentle as it opens the cell and lets them out, but Brock mentions that Togepi could not have used Teleport, but Substitute would have created the desired effect. Having been unmasked, Togepi turns with an evil grin. Meowth tries to attack with Fury Swipes, but Togepi uses Attract to not only stop Meowth, but capture Pikachu, Piplup, and Croagunk as well; however, it has no effect on Yanmega. After Togepi gets the affected Pokémon onto the elevator and up, the humans wonder why. Jessie ponders this, but Brock explains that Attract will only work against the opposite gender. James adds that it worked against Meowth, who they know is male, and since that makes Togepi female. Jessie ponders this for a second before coming to the conclusion that Yanmega is female. Since the elevator is inaccessible, James leads them to the stairwell.
As they ascend, the building starts to shake as at the top, Togepi leads them to the control room as Meowth reveals the true nature of the structure: it is a spacecraft. The tower's outer structure comes apart and unveils a rocket ship. Togepi takes command of the bridge and has Meowth activate the boosters and sends the ship rocketing into space. The rocket takes them out into orbit as they plan to head away from the planet. The humans break onto the bridge and Brock has Happiny use Pound to snap everyone out of infatuation, only to have Togepi recast Attract. Happiny and Togepi squabble and fight as Pikachu points that a Rayquaza is approaching. It fires Hyper Beam, and though it misses, the force sends the ship hurtling back towards the atmosphere. The ship jolts and snaps the Pokémon out of infatuation as the power goes out and the exterior of the ship starts to heat up from reentry.
While Happiny and Togepi continue to skirmish, James, having received a real rocket for his 10th birthday, takes control of the ship. Ash, Brock, and Dawn also offer their assistance. As Meowth removes a panel to the emergency generators, James has Pikachu power them up with Thunderbolt and Buneary to cool down the exterior nose cone by firing Ice Beam around the bridge. However one of the ship's maneuvering rockets explodes, making it unstable, leaving James clueless. Brock suggests to have Grotle and Piplup use Energy Ball and Bubble Beam to create explosions outside to stabilize the ship, which works. James deploys the parachute and the ship slowly floats downward. He sets the controls to auto-pilot when Togepi fires Flamethrower at Happiny and Happiny deflects it upward with Pound, incinerating the parachute and sending the ship into free fall. Just as they are about to crash boosters-first, Togepi uses Psychic to set the ship down gently for the last few meters. Togepi glares back at Happiny and states that they'll continue their battle another time. Meowth repeats in disbelief that Togepi is tired and is gonna go home as she walks off the bridge. She gets clear of the rocket just as the ship disintegrates.
In the wreckage, Dawn considers the fact that even Togepi can have a darker side, but Brock reassures her that this Togepi was most likely an exception. Ash on the other hand can't help but think about the fact that the gang got to travel to outer space. Picking themselves up and dusting themselves off the gang continue onto Lilypad Town. Meanwhile Team Rocket are trapped by the debris, where they will be staying for the time being. As for Togepi, she walks away laughing, ready to cause misery again.