In a different dimension, Legendary Pokémon Dialga and Palkia clash and start fighting each other. A trio of shadowy figures observes them from afar, declaring that soon, all Pokémon will belong to Team Rocket.
Meanwhile, in Sandgem Town, Dawn is prepping her Pokémon for some Contest training, but her Piplup is dozing off. Dawn wakes him up and berates him for slacking off lately. The frustrated Piplup runs off into a nearby forest. Dawn chases after him, but suddenly stops in surprise when she sees someone who looks exactly like her grabbing Piplup and walking through a strange portal. She tries to catch the person's attention, but before her doppelgänger can do more than turn around, the portal shrinks away and vanishes. Alarmed, Dawn immediately makes a phonecall to Ash and informs him of what's happened. Professor Cerise tells Ash and Goh that similar cases of Pokémon disappearing without a trace have been happening all over Sinnoh lately. As Ash and Goh agree to go to Sinnoh to investigate the disappearances, Chloe, having overheard that Dawn's in trouble, declares that she'll come with them too.
Ash, Goh, and Chloe travel to Sandgem Town, where they find Dawn being upset over losing Piplup. Ash manages to restore Dawn's optimism with some croquettes he bought, after which she explains the details of what happened. Hearing that the person who took Piplup looked exactly like Dawn makes Goh and Chloe remember a recent case of them meeting someone who looked exactly like Chloe. However, Dawn thinks this case is different, as the person had disappeared into a strange shining hole after taking Piplup. Ash wonders it was an Ultra Wormhole, and while Dawn is uncertain, Officer Jenny had afterwards told her of the other disappearances and that they've started calling the portals "Gates" for now.
Just then, Team Rocket swoops in with their Meowth balloon and snatches Pikachu with a claw attached to a fishing line. Their moment of triumph is cut short when Ash has Lucario set Pikachu free and Goh uses Inteleon's Snipe Shot to puncture the balloon, sending the trio blasting off again. However, only moments later, a Gate opens before them, from which another Team Rocket trio, this one clad in black suits of armor, emerges. Their Meowth fires a Dark Pulse at Lucario and Inteleon, before their Wobbuffet fires an electric net at each of them, ensnaring the two Pokémon as the villains begin to retreat back through the Gate with their quarry. Ash, Dawn, and Goh give chase, but Meowth's Dark Pulse throws Ash off, leaving him and Chloe behind as Goh and Dawn dive through the Gate a moment before it vanishes.
On the other side of the Gate, Dawn and Goh find themselves in a place that looks almost exactly like where they just were, except that there's aurora in the sky. With Team Rocket nowhere in sight, Dawn decides the best course of action would be to go see her home for clues. They travel to Dawn's home in Twinleaf Town, where Dawn notices that the garden next to the house is devoid of blooming flowers, which had been there this morning. Goh realizes that the park they had appeared in was devoid of them too. Thinking back, they realize another reason why the place they're in seems so strange: there are no Pokémon either. They enter the other Dawn's room, where they learn that she's placed second in a Sinnoh League tournament, showing that she's a different person. Despite their differences, though, both Dawns have a Piplup as their partner, as proven by photos Goh and Dawn find. Just then, they hear footsteps approaching, which turn out to be from the other Dawn, carrying Dawn's Piplup. As soon as Piplup sees his real Trainer, he runs back into her arms.
The other Dawn explains to Dawn and Goh that Gates connect different worlds, so she and Dawn are the same person, just from alternate realities. She apologizes for taking Dawn's Piplup, admitting that she had wanted to return it, but the Gate had closed before she could do so. Goh asks why there don't seem to be any Pokémon in this world. In response, the other Dawn takes them to the Sandgem Town Pokémon Center and shows them an Egg that used to be her Piplup. The whole Pokémon Center is filled with Eggs that used to be Pokémon. One day, Gates had started appearing in Sinnoh, and soon afterwards, Pokémon had started to forget their moves, then turn back into their previous forms, and finally revert all the way into Eggs. Professor Rowan has gathered the affected Eggs and Pokémon to this Pokémon Center while trying to figure out the cause behind everything. When the other Dawn had seen Dawn's Piplup through a Gate, she had been reminded by her own Piplup so much that she had been unable to resist herself and taken it. The other Dawn apologizes for what she's done, as now Dawn and Goh's Pokémon will suffer the same fate as the Pokémon of this world, causing Dawn to panic at the thought of losing Piplup. Thinking about everything they've heard, Goh figures that time and space are being distorted, and recalls that there were some Pokémon that had something to do with those concepts. After a moment of thinking, Dawn remembers that the Pokémon in question are Dialga and Palkia.
Meanwhile, in the regular world's Sandgem Town, Ash and Chloe are wondering where Dawn and Goh are. Based on a novel she's read, Chloe theorizes that the Gates could connect to different worlds. They start wondering if there is a Pokémon with the power to travel between worlds, and Ash quickly remembers that Palkia can do so. Chloe consults her Rotom Phone, which confirms their assumptions about Palkia's ability to travel between dimensions, and says more information about it can be found at the Canalave Library. Ash and Chloe travel to the library, but before they can find anything, they're spotted by Cynthia. Ash introduces Chloe to her and tells her that they're looking for information about Palkia. Understanding they're looking into the recent Pokémon disappearances, Cynthia tells them about Dialga and Palkia, as well as the Pokémon said to have created them, Arceus.
Ash, Chloe, and Cynthia exit the library while coming to the conclusion that Palkia is behind the recent incidents. Suddenly, the alternate version of Team Rocket appears next to them to steal more of their Pokémon. Cynthia sends out her Garchomp, whose Dragon Claw clashes with Meowth's Slash. Cynthia tells Garchomp to follow up with Outrage, but the Mach Pokémon suddenly becomes unable to use the move. A similar result occurs when Ash tries to have Pikachu use Thunderbolt. Wobbuffet launches a pair of electric nets to capture the two Pokémon, but Cynthia calls out Kommo-o, whose Outrage tears the nets apart. Seeing their capture operation is being jeopardized, Team Rocket decides to retreat, with Ash and Chloe leaping through the closing Gate after them. The regular Team Rocket, having landed on a nearby tree following their blast-off, witness all of this, and soon see a Gate opening right next to them as well.
Ash and Chloe discover themselves in the world on the other side of the Gate, but Team Rocket has gotten away. Like Goh and Dawn before, they quickly notice the aurora in the sky and the absence of flowers and Pokémon. Always a positive thinker, Ash doesn't worry about a way to return to their world and instead decides to focus on finding Dawn and Goh. He runs over to a nearby person to ask them something, but stops in surprise when he realizes the person is his alternate self. In another dimension, Dialga and Palkia continue their clash.