A young boy in one of the polar regions finds a group of SphealSealeo and Walrein, when a meteor crashes down, frightening the Pokémon and making them run towards the sea, trapping the boy in the middle of them. His dad and Yuko, who are both part of a team of researchers manage to save him, when a Deoxys appears from the middle of the crash site, having come to Earth on the meteor. However, Rayquaza sees this as an invasion of its territory and attacks. A battle starts between the two, destroying most of the equipment of the researchers. Rayquaza ends up blasting Deoxys to the bottom of the ocean. A green stone found at the crash site is taken back with the researchers on a helicopter.
Four years later, lasers are being fired by the researchers at the green stone, which starts to glow, but there is not enough power for it to do anything else. Meanwhile Deoxys has regenerated and bursts through the ice.
Soon afterwards, Ash Ketchum and his friends arrive in LaRousse City. At the same time a Plusle and Minun are playing with a high-tech bin, with a Munchlax cleaning up litter.
Ash and co. are greeted by a security robot and given passports. Some people save Ash from going the wrong way on a moving side walk, who introduce themselves as SidRafeRebecca and twinsAudrey and Kathryn.
Ash arrives at the Battle Tower, and tries to ask directions from a boy about the same age as himself, who runs away, seemingly scared by Ash. They then find themselves in the middle of a battle, whereTory, the boy Ash was following, reveals he has no Pokémon. They are up against Sid and Rafe, so Ash loans Tory his Torkoal. They lose badly, and Tory runs off after his dad congratulates him on taking part in the battle. Then Yuko tells Ash what happened four years ago, and that Tory is scared of Pokémon. Ash decides to try to help him overcome his fear. Tory, after freeing the Minun from earlier from a bin with a stick, goes into the gardens to meet with a strange green light.
Deoxys has reached LaRousse City, and is creating strange lights in the sky, resembling an aurora. Meanwhile, Team Rocket is trying to get hamburgers from a machine, but as they don't have passports and are trying to destroy the machine, they get attacked by a security robot instead. By this point, Ash and the others find Tory, and Brock offers to cook everyone a meal. Ash tries to get Tory to touchPikachu, but he runs off again. Meanwhile, Deoxys creates the aurora again, and Tory finds Ash, who calls out all of his Pokémon. Tory is having fun, but still can't bring himself to touch Pikachu. Then Tory takes them, and the people from earlier, to meet the green light. However, Rayquaza is heading towards LaRousse City in pursuit of Deoxys, so Tory's father decides to evacuate the city, but Ash, Tory and the others get trapped inside the building. Deoxys makes copies of itself and tries to carry the people being evacuated away. It creates a force field around LaRousse to stop Rayquaza from getting in. Ash and the others try to get out but are attacked by the multiple Deoxys. Plusle, Minun and Munchlax find Ash and his friends. They realize they need food and water, so they go outside and Pikachu shocks a hot dog machine, but again, they get attacked by Deoxys, who steals Minun and the hot dog machine.
Back inside, Tory tries to touch Plusle, but still can't do it. Brock finds water in some boxes. Rafe and Rebecca watch Deoxys take Minun into a domed tower, then drop the hot dog machine into the water. Rayquaza is still trying to break through the forcefield. Rebecca and Yuko try to work out why the Deoxys dropped the hot dog machine. The others are all trying to get some rest, wrapped up in blankets on the floor, when Surskit becomes agitated and runs around waking everyone up, warning them Deoxys is trying to get in. They run to an underground laboratory, where Yuko tells them that a second Deoxys is dormant inside the green crystal. Tory's light appears from the crystal, and they work out the light and the aurora have the same light pattern. The green one is saying "friend" and the other one "where are you?" So Deoxys is just looking for its friend. Rayquaza is still attacking the barrier.
They decide to try to wake the second Deoxys up, but they don't have enough power. They go off to try to make extra power, but Deoxys lands in front of them. Ash tries to tell them that they're not enemies, but it doesn't work, so everyone tells their Pokémon to attack. Rafe holds the Deoxys off long enough to let Ash escape. Rayquaza then breaks through the force field, and Rafe and Blaziken get carried off.
Ash manages to get to the building where the others are being held, where Rafe is starting a plan to get them out of there. Rayquaza and Deoxys are about to battle. Pikachu and Plusle Thunderbolt the doors of the dome, freeing everyone inside. Meanwhile, Rayquaza is chasing Deoxys.
Ash, Tory, Plusle and Minun go back to the lab, while the others try to power up the windmills to get more electricity, using ropes, Blaziken jumping from one blade to another, various Water Pokémon using Water GunFlying types using GustMetagross using Confusion and Team Rocket pedaling a machine.
Tory turns on the lasers to wake up the green Deoxys, but they're still 20% short on power, so Pikachu, Plusle and Minun shock the machine and it works. The stone grows into a Deoxys, who makes Ash and Tory float out of the building. However the other Deoxys is about to finish off Rayquaza after tackling it to the ground and continuing to attack it, and the second Deoxys comes and protects the Rayquaza from the attack. They both change Forme and release an aurora after being reunited. Then Rayquaza comes out of the ground, and is going to again attack the two Deoxys.
Because of the increased power, the block security robots power up and go on overdrive, trying to attack Rayquaza. It gets buried under the robots and, when the Deoxys try to help, they get buried as well.
Just then, Tory's father appears on a screen, saying the only way to stop the blocks is by presenting a passport to the chief robot, allowing them to regain control and shut it down. Ash and Tory ride on a hot dog machine to near the tower they need to get up, but miss. Just then, Munchlax, who was hiding in the bottom of the machine, gets out and evolves, allowing Ash to step over it to a nearby tower. Pikachu realizes the only way to get to the tower they need is by stepping on the block robots. Ash follows, but drops his passport. Tory throws him his, and Pikachu leaps off to bat it up to Ash. He manages to give the robot the passport, allowing Tory's dad to power down the robots. But Plusle and Minun, who are at the top of a pile of blocks with Tory, fall off. Tory reaches out to grab them, but falls off too. They get saved by Deoxys. Tory, who had never touched a Pokémon before, finally touches a Pokémon. Rayquaza befriends the Deoxys after they tried to save it from the blocks, and they all fly together out of LaRousse City to find the others. The Deoxys then go back home.