With Max and Meowth taken by Deoxys, Ash and the others head back to the Pokemon Center to devise a plan. Solana manages to fix their Pokeballs and so they head out in search of their friends. In Deoxys' world, it explains to Max (through Meowth) that it is very lonely and confused. However, the geometric imbalance is starting to create chaos in the world, this pain causes Deoxys to start attacking everybody. Their only hope is for Solana to use the Capture Styler on Deoxys, but it only works when Deoxys is in normal form. Now the others must battle to save themselves from Deoxys and wait patiently for the right time to capture it.
At the Pokémon Center, Jessie, James and Mime Jr. beg the heroes to bring Meowth back. The heroes agree to a truce to bring Max and Meowth back. Team Rocket goes, but Nurse Joy asks where are they going, so Team Rocket are sad again because they do not know where. Solana asked the Rangers via the device about Solowind and got a response. Solowind is sun's wind - the warmth and the light Earth receives. She got an answer that the dark spots on the sun increase and decrease each 10 years - this seemed to have caused the geomagnetic disturbance, but Solana tells them it is in the cave they were before that is the source of the disturbance.
Max and Meowth are in a strange space. Meowth does not remember he was possessed and the Deoxys arrives. Max demands to know where they are, so Deoxys uses Meowth to communicate. It tells they are in its room, not the cave. It came from space, being transported by the meteorite. It was cold, but Deoxys heard a loud voice - the meteorite crashed. Deoxys was free, but again was lonely. Max tells it is not lone anymore, with all the Pokémon on the planet to be with. The heroes, Solana, Nurse Joy and Team Rocket. Brock sees no geomagnetic disturbance, meaning Pikachu and Plusle are okay. May and Jessie yell for Max and Meowth, but with no response. So, they send Sceptile, Marshtomp, Swellow and Combusken to help. Ash asks what will do when they encounter Deoxys again, so Solana thought she could capture it and use recover, as it is in pain.
They suddenly feel the cave shaking again and the geomagnetic disturbance is present. Pikachu comes inside Ash's bag and Joy takes Plusle. Inside Deoxys' room, Deoxys feels pain again. The link between Deoxys and Meowth is broken, but Meowth does not know he was possessed. Deoxys begins to feel weak, while the heroes spot a portal where Meowth, Max and Deoxys are. Deoxys comes out, though Plusle and Pikachu feel bad. The meteorite begins to act strange and the markings on Brock's device tell the geomagnetic disturbance is very powerful, as it is destroyed. Solana now knows the meteorite caused the disturbance. Team Rocket, Nurse Joy, the heroes and Solana run away and the meteorite explodes.
Later, the Pokémon wake up everyone. Solana spots a glow from the cave and realizes the sun energy with the energy from the meteorite made a new Deoxys. Deoxys was feeling pain because of the combined energies and feld to a portal. May thinks Deoxys wanted to tell them all this time and Meowth was the translator. However, they spot a thunderstorm approaching. Deoxys re-appears and Solana goes to capture it, but needs the other Pokémon to help so it can come in normal form. Deoxys changes to Attack form and uses Psycho Boost, so Sceptile uses Bullet Seed, Combusken Flamethrower and Marshtomp Water Gun. The attacks do not stop Psycho Boost, though everyone evades the attack. Deoxys uses Psycho Boost more and more, then goes to Speed form.
Sceptile uses Bullet Seed and Swellow follows Deoxys. Swellow uses Aerial Ace, attacking Deoxys, and uses Quick Attack, but misses. Swellow uses Aerial Ace to dodge, but Deoxys managed to hurt Swellow. The meteorite's energy bursts and the wind gets stronger. Sceptile launced SolarBeam, but Deoxys dodges. The meteortite bursts, making more disasters. Deoxys changes forms at a rapid pace, one it can't control. Solana goes to capture Deoxys, but Deoxys evades. Max and Meowth bounce on the strange objects in Deoxys' room as the meteorite bursts. May and Jessie gout Meowth and Max out of Deoxys' room. Sceptile attacks Deoxys, gets on it and launches SolarBeam. Deoxys goes to normal form and Solana goes to capture Deoxys. This time, Solana captures Deoxys and Deoxys recovers, renewing itself.
The meteorite explodes, but Deoxys uses Safeguard to protect everyone. The disaster ends - the geomagnetic disturbance is stopped. Deoxys uses Meowth to communicate, telling Max it is his friend. It decided to go to see the world. Deoxys goes away and makes an aurora. Solana reports to HQ she completed her task.
- In one scene Sceptile fired SolarBeam, but later Ash told Brock Sceptile did not fired the beam.