While taking a little time off on their way to Sunyshore City and Ash's next Gym Battle, our heroes discover Team Rocket's Meowth. The dazed Pokémon has been separated from Jessie and James after a rough run-in with Team Galactic! After explaining the situation, Meowth and our heroes head out to Team Galactic's secret base to rescue Jessie and James, as well as Looker from the International Police.
As Team Galactic continues to put the pieces together to accomplish its evil plans, our heroes confront the mysterious Jupiter of Team Galactic. She informs them she is aware of their previous encounters with the three lake Pokémon Mesprit, Azelf, and Uxie. This news bewilders our heroes all the more. Meanwhile, the gang (along with Meowth) rescues Looker, who has been trapped in a cell with Jessie and James. Team Galactic gets away, leaving Looker and our heroes still wondering what the evil organization is up to.
While trying to unravel the mystery, Looker discovers an object left behind by Team Galactic that, upon examination, destroys every bit of data the International Police have collected on them! That leaves everyone frustrated, but doubly determined to get to the bottom of Team Galactic's evil plans, as Pokémon Hunter J prepares to catch the very same three lake Pokémon...
A Galactic Grunt, later revealed to be Looker, is attacked by Jupiter while on a counter-operative mission at the Fuego Ironworks. Skuntank is about to use Slash, but an explosion is triggered.
Meanwhile, in the Floaroma Town Pokémon Center, Ash and his friends are watching television, learning that the next Pokémon Contest will be held in Daybreak Town, located east of Mt. Coronet, and will follow the Double Performance format. The group hit the road, following Route 205, when Pikachu and Piplup see something in the flowers. Closer inspection reveals it is Meowth. Seeing as he is badly injured, Brock heals him with a Super Potion. Meowth explains that Team Rocket was walking, feeling hungry, when they saw Team Galactic's helicopter. They chased after it and arrived at a factory which Brock checks on his Pokégear and identifies it as the abandoned Fuego Ironworks. Team Rocket climbed a ladder and saw Jupiter and Looker. The trio rushed to Looker’s aid, with James's Carnivine Vine Whip stopping Jupiter’s attack. Skuntank managed to break free and Jupiter commanded the Golbat to attack. The resulting explosion blasted Meowth off, while Jessie and James were taken hostage by Jupiter. After being bandaged, Meowth proceeds to return to Fuego Ironworks to help his teammates. Ash’s group wants to help too, prompting Piplup and Pikachu to catch up with him but Meowth warns them off with Fury Swipes, reminding them that they're enemies. Dawn replies that they're actually in this for Looker since he had helped them out back on Mt. Coronet.
Back at the Fuego Ironworks, Jessie, James and Looker are locked up inside a prison cell. Jessie spots Skuntank look at her smugly, but gets shocked after she touches the door. Looker adds that the entire facility is rigged with traps, with even Poké Balls not working. He tells Team Rocket that Team Galactic has been secretly using Fuego Ironworks to make something; the Red Chain. Over on Mt. Coronet, Saturn's Toxicroak uses Rock Smash to break down a part of the mountain, revealing a huge, silvery spherical object. The Spear Key reacts to the object, confirming to them that they've finally found the Gateway to the Spear Pillar. Cyrus watches from the comfort of HQ, and orders Saturn to lockdown the area until all preparations are ready. Jupiter and Charon soon learn that Spear Pillar has been found and receive new orders to deliver the Red Chain. A Team Galactic Grunt then informs Jupiter and Charon that an unidentified flying object has been detected near the Factory perimeter which turns out to be Ash, Dawn, Brock, Pikachu, Piplup, and Meowth approaching Fuego Ironworks in Meowth's Balloon. Upon being confronted by a group of Golbat, Ash's Pikachu, riding on Staraptor, and Dawn's Pachirisu on Gliscor, take them out with Thunderbolt and Discharge.
The group prepare to land on the Fuego Ironworks rooftop, only to be greeted by Jupiter who has her Skuntank use Flamethrower. Piplup counters with Bubble Beam. Jupiter admits the kids are good at appearing out of nowhere and suggests they join Team Galactic, though they refuse. Meowth asks about Jessie and James and Ash asks where Looker is. Jupiter doesn't give them any information, but to Dawn she says "Oh, Mesprit", to Ash she says, "Azelf," and to Brock she says, "Uxie.", and the group recall their encounters at Lake Verity, Lake Valor, and Lake Acuity. Jupiter is furious and admits that Team Galactic were supposed to have synchronized with the Lake guardians. Then, a group of Golbat use Air Cutter on Pikachu and Staraptor. Pikachu counters with Thunderbolt while Meowth rushes forward and uses Fury Swipes. Skuntank tries a Flamethrower though Piplup counters with Bubble Beam. Gliscor and Pachirisu land behind Jupiter and Skuntank and Pikachu and Staraptor land on the side. Jupiter orders a Toxic, forcing everyone to cover their mouths from the hazardous fumes, allowing Jupiter to escape in a helicopter. Jupiter still cannot understand why the Lake guardians chose Ash and his friends, while Charon chastises her for being jealous. She snaps back and asks about the Red Chain. Charon assures her it's safe, and notes that it is stored within the helicopter.
Meanwhile, Meowth and the group returns the attention to finding their missing friends. They soon locate Looker, Jessie and James in their cell. Piplup and Pikachu use Bubble Beam and Thunderbolt on the door and it breaks. Looker thanks them and Team Rocket reunite then leave to track Team Galactic down. Seeing as Jupiter is gone, Looker decides to examine the Fuego Ironworks for clues as to Team Galactic’s plan. With his special glasses, Looker leads the group down an elevator shaft and to an altered manufacturing area. A gleaming shard, a piece of the Red Chain, attracts Looker’s attention. At the Floaroma Police Station a machine examines the shard and transmits the data to International Police HQ. But within a few seconds the shard glows before destroying the device. The shard turns out to be some sort of bomb as they receive a call from the International Police informing them that their entire database had been wiped out during the analysis. Looker departs from the station infuriated by the setback.
In the meantime, Cyrus and Team Galactic are on their way to the Spear Pillar with the Adamant Orb, Lustrous Orb, and Red Chain in their possession. Cyrus then contacts Pokémon Hunter J with new orders – to capture the Lake guardians.