With Meowth and Max both vanished after an encounter with Deoxys, Team Rocket makes a truce with the twerps so they can rescue their favorite talking Pokémon. Solana suggests that recent solar winds may be linked to the strange geomagnetic activity focused on the meteorite cave, so our heroes return to the cave in search of Meowth and Max. Those two are currently floating in a strange space along with Deoxys. Deoxys possesses Meowth to explain to Max how it came to this world on a meteorite, but ended up in the cave with no friends.
When Solana and the group reach the meteorite, they realize it's the source of all the strange phenomena they've witnessed—and there's tremendous energy building up around it! Rescue has to wait as everyone tries to get clear, but an explosion from the meteorite throws everyone out of the cave. Deoxys shows up and Solana realizes that these chaotic energies are what's causing Deoxys pain, but she can't capture it to help it unless it's in Normal Forme.
Everyone pitches in with their Pokémon to keep Deoxys distracted until it returns to Normal Forme. Meanwhile, a portal to Deoxys' dimension reappears, with Max and Meowth floating inside. They're not feeling too great, either! Team Rocket and May rescue them from the weird fissure just before it closes again. Solana finally captures Deoxys and has it heal itself with Recover. But the energies are still going haywire, so just as the meteorite finally explodes, Deoxys uses Safeguard to protect everyone. Once the smoke clears and things calm down, Deoxys says goodbye to Max and flies off to explore, now knowing that there are many Pokémon in the world and it's no longer alone.
After the events of the previous episode, Deoxys takes Meowth and Max into another dimension. Ash's group returns to the Pokémon Center as Team Rocket begs for Meowth's return. They decide to help recover Meowth and Max. Solana sends a message to Ranger base, receiving a reply that every ten years, Sunspots intensify and directly increase the solar wind strength, causing amplified energy matching the geomagnetic disturbance. She shows a wave graph and pinpoints the source on a map.
Max and Meowth wake up in an alternate dimension as Deoxys appears. Deoxys takes over Meowth and talks to Max. They are in his room because Deoxys hates the cave. Deoxys mentions that he came from space with the meteorite, mentioning that it was small, cold and soundless. Deoxys wanted to hear a voice, but it woke up from the meteorite impact. A flashback shows the meteorite impact and that Deoxys was still alone after crashing. He wanted to find a friend, but nobody was in the area. Max assures Deoxys that he does not have to be alone, showing all the Pokémon on the planet.
Ash and his group check out the cave, the geomagnetic reading is still flat. Brock brings out Marshtomp, May summons Combusken and Ash deploys Swellow and Sceptile. They all split up and search the cave. Solana mentions that she must capture Deoxys and have it use Recover to heal itself. Another disturbance spikes and Pikachu suffers. Ash has Pikachu climb into his backpack while Nurse Joy takes Solana's Plusle. The group presses forward. Back in Deoxys' room, Deoxys writhes in pain as it releases Meowth from control. Deoxys opens a hole back to the real world as the Pokémon and Ash's group return to the meteorite, noticing Max and Meowth in the alternate dimension. Deoxys comes out as another solar wind increases the disturbance. The meteorite begins to sparkle with energy as the geomagnetic reader shorts out. The meteorite is the source of the disturbance and is teeming with energy. The meteorite explodes with energy as everyone runs, getting caught in the explosion.
Everyone winds up outside as the Pokémon wake up the humans. They notice the meteorite energy from outside as the cave. Solana mentions that the meteorite has so much energy and the solar wind energy combined is causing Deoxys pain. Deoxys had to get away from it by entering an alternate dimension. Nurse Joy mentions that it's ironic that Deoxys' meteorite is causing it pain. Static discharge clouds appear as the meteorite's energy is lowering the atmospheric pressure and destroying the geomagnetic balance. Solana prepares her Capture Styler, but she needs their help to restrain Deoxys. Deoxys attacks with Psycho Boost as Sceptile fires Bullet Seed to intercept. Combusken uses Fire Spin and Marshtomp uses Water Gun try to stop the attack, but it fails, everyone dodging. Deoxys attacks everything around, as Solana is unable to track Deoxys. Sceptile fires Bullet Seed, but it dodges. Swellow follows Deoxys, switching to Speed Forme, but it turns to face Swellow. Swellow uses Aerial Ace and Quick Attack, but it dodges. Deoxys speeds towards Swellow, but Swellow tries to use Aerial Ace to dodge, but Deoxys hits and sends it to the ground. The meteorite creates more energy as more atmospheric pressure drops. Sceptile fires Solar Beam, but Deoxys dodges as the alternate portal opens, showing Max and Meowth. The meteorite explodes with energy as it begins a chain reaction, harming the wild Pokémon. Deoxys flies around in a rage as Max and Meowth are stuck. Deoxys continually changes formes, but Deoxys gets hurts from the energy. Deoxys finally switches to Normal Forme as Solana attempts to capture, but it dodges and escapes. Max and Meowth bounce around in the alternate dimension as May and Team Rocket reach the portal. May pulls Max through as Jessie pulls Meowth through.
Deoxys writhes in pain as Sceptile tries to hit, but Deoxys speeds away. Sceptile grabs onto Deoxys and fires Solar Beam into its back, sending it down and changing Deoxys to Normal Forme. Solana makes another capture attempt, this time succeeding. Solana has it use Recover, healing itself. The meteorite explodes with more energy, consuming the valley. Deoxys steps in front of the blast wave and uses Safeguard to stop the wave. The clouds and wind subside as air pressure returns to normal, the disturbance gone. Deoxys takes Meowth and speaks, wanting to explore the planet more, thanking Max and taking off. The aurora returns as everyone watches. Solana reports in and mentions her mission is complete.