Resuming from the end of the previous episode, Ash and Chloe come face to face with an alternate version of Ash in an alternate Canalave City, with Chloe explaining to him that they came from a different world similar to this one. When the alternate Ash spots Pikachu, he cries and hugs him before revealing that his own Pikachu has reverted into an Egg, as if time itself was flowing backwards. Ash panics at the thought of the same happening to his Pikachu, and alternate Ash suggests they go to Sandgem Town.
After a ride with Ash's Dragonite and Gengar, Ash, Chloe, and alternate Ash arrive at the Sandgem Town Pokémon Center, where they find all the Eggs stored there being loaded into a large truck by Professor Rowan, against Nurse Joy's objections. Just as Goh, Dawn, and alternate Dawn come out of the Pokémon Center and reunite with Ash's group, another Professor Rowan suddenly appears and demands to know what's going on. The first "Professor Rowan" and his "assistant" remove their disguises, revealing themselves as this world's Jessie and James. They escape with the Eggs while Meowth briefly stays behind to keep anyone from following them. Ash and Goh send Pikachu and Cinderace to battle him, but before they can even attack, the time reversal turns them back into a Pichu and a Raboot. Alternate Ash and Dawn recommend they should recall their Pokémon to slow down the reversal process, which they agree to do, while Ash places Pichu in his vest pocket.
Professor Rowan warns the children that the time reversal will affect not just plants and Pokémon, but humans as well, alarming the group. Understanding that Dialga and Palkia are behind these events, Professor Rowan directs the group to the Spear Pillar atop Mount Coronet. Ash calls out Dragonite and Gengar to take him and Goh there, but they immediately turn back into Dragonair and Haunter, showing that the time reversal is getting faster and faster. Ash recalls his Pokémon while Goh sends out Flygon and Aerodactyl. Dawn and Chloe also come along, but since there's not enough room for alternate Ash and Dawn, they must follow them behind. As they take flight, Goh gets an idea and makes a call on his Rotom Phone.
Meanwhile, the regular Team Rocket has arrived in this world's Canalave City through a Gate. Jessie enjoys her skin feeling smoother than usual, but the good feeling about their current situation begins to fade as Meowth starts losing his ability to talk and Wobbuffet suddenly reverts into Wynaut. While Ash and his friends arrive at the Spear Pillar and leap through a Gate they find there, alternate Ash and Dawn are approached by this world's Goh and Chloe. As they head to Mount Coronet together, alternate Ash and Dawn note the suits of armor alternate Goh and Chloe are wearing. They explain that, after noticing how Team Rocket's Pokémon weren't being rewound, alternate Chloe hacked into their database and constructed them and their Pokémon the same kind of suits the villainous team had to protect them from the time reversal.
Ash and his friends find themselves in an odd, dark dimension, where they immediately find Dialga and Palkia locked in a fierce clash and opening Gates in the process. Before they can do anything to stop them, alternate Team Rocket appears before them and sends out their Pokémon. Ash and Goh do the same, but the time reversal immediately causes all of their Pokémon to revert into Eggs. In Team Rocket's cage, Ash and Goh see Lucario and Inteleon, who quickly start to devolve, along with the other Pokémon held in the cage. Alternate Jessie and James reveal that they are the ones responsible for Dialga and Palkia's battle, all thanks to the Red Chain, which contains the power of Arceus. Thanks to Palkia creating Gates and all life forms being rewound by Dialga, Team Rocket plans to collect all the reverted Pokémon and Eggs for themselves. And once Dialga and Palkia have tired themselves out with their battle, they will catch them and raise the stolen Pokémon and Eggs to serve Team Rocket, making their conquest of the world all the easier.
Just then, alternate Goh, Chloe, Ash, and Dawn arrive to join the battle. Ash and his alternate self head forward to break the Red Chain, while, Goh, Dawn, Chloe, and their counterparts battle Team Rocket. However, amidst of the battle, Dialga's time reversal strikes everyone with such force that even the protective suits break. The surge of power sends Team Rocket blasting off through a Gate, turns Ash, his friends, and their counterparts into toddlers, and reverts all of their Pokémon into Eggs.
With no Pokémon with them anymore, the group seems to be out of options for how to stop the fight. Ash decides that they should send out their feelings to Dialga and Palkia to make them stop, and alternate Ash suggests they do the same with Arceus as well, since it was the one who created Dialga and Palkia, and must have the power to return everything to normal. Through Gates in both the regular and alternate world, people join in on praying for their Pokémon to be brought back. Reacting to the group's desperate pleas, a shining image of Arceus appears from the Red Chain and makes it disappear, finally stopping Dialga and Palkia's fight. The two Legendary Pokémon immediately start undoing the results of their battle and send the group to alternate Sandgem Town, where they return to their normal ages and their and everyone else's Pokémon are returned to normal, with Meowth also regaining his ability to talk. With everything returning to normal, Ash, his friends, and their Pokémon are pulled back to their own world, bidding farewell to their alternate selves.
Arriving back to their own world, Ash and his friends, secretly followed by the Team Rocket trio, are happy to see that everything is back to normal, and happily rush to greet Cynthia. In the dark dimension, Dialga and Palkia part ways.