The Chasers of Project Mew, having gotten split up into two groups during their exploration of Faraway Island due to unforeseen circumstances, are now facing a Groudon and a Kyogre, respectively. Groudon quickly overpowers Quillon's Weavile, but is saved from being struck by its Precipice Blades by Gary distracting it. Groudon then promptly turns around and leaves. Quillon feels something is off with Groudon and urges Gary to follow it with him. With the other group, Danika and her Azumarill are no match for Kyogre. Goh and Horace attempt to distract Kyogre with flares, only to be sent flying by its Origin Pulse. When Kyogre prepares to attack again, Grookey, unable to just stand back and watch any longer, jumps in and hits Kyogre with Wood Hammer. While it fails to deal significant damage, Kyogre still turns around and swims away. The Chasers pursue it, with Goh thanking Grookey for helping them along the way.
The Chasers follow the Legendary Pokémon into a large open area at the center of Table Mountain, where they spot each other and the two Pokémon heading towards each other. Groudon and Kyogre clash, and as soon as they do, they suddenly start glowing and mold together into one being, which is revealed to have been a disguised Mew all along. Mew teleports onto a glowing, floating rock at the center of the area, which releases pulses of light onto other rocks in the area, causing them to glow as well, much to the enjoyment of the local wild Pokémon. When the Chasers approach the floating rock, its glow brightens to a blinding level. Goh suddenly finds himself floating in space, where he witnesses a supernova, the birth of a galaxy, the formation of the solar system, and even the birth of the Pokémon world. Rayquaza flies by, causing Goh to fall into a prehistoric sea, where he witnesses the life of ancient Pokémon, before being pulled out of the water and flying towards Faraway Island alongside Mew, who then unexpectedly disappears and lets him fall.
Goh snaps out of his vision just as suddenly as it had begun, and it turns out all the Chasers had actually experienced the exact same vision as well. Danika theorizes that the floating rock is actually a crystallization of the memories of the universe, but as soon as she touches it, it stops glowing and falls to the ground. The other rocks also stop glowing as a result, leading to the wild Pokémon to start bickering with each other. Professor Amaranth suddenly contacts them, revealing that their electronic devices, including communication equipment and Poké Balls, are working normally again. Amaranth informs the Chasers that the Psychic energy sensor is reacting, and they look up to see Mew floating above them, observing as the bickering between the wild Pokémon escalates into an outright fight. Mew unleashes a Thunderbolt at all the Pokémon, with Quillon and Danika sending out their respective Urshifu to defend the group from stray bolts of electricity. Mew starts using Air Slash on the Wushu Pokémon, who are quickly overwhelmed and defeated by the Mythical Pokémon's power. The Chasers send out a new set of Pokémon to try to stop Mew, though Goh does so very reluctantly, as he feels Mew is only playing around. A massive Shadow Ball from Mew easily overpowers the Chasers' Pokémon's counterattacks and Horace's Gardevoir's Light Screen, resulting in lots of damage on them and even the surrounding Pokémon. Goh's pleas for Mew to stop are ignored, and it proceeds to easily defeat the Chasers' Pokémon with another devastingly powerful attack.
In order to prevent Mew from hurting the other Pokémon more, the Chasers, aside from Goh, send out a new wave of Pokémon. While this wave is getting defeated as easily as the previous one, Goh desperately tries to think of a way to make Mew stop. He then remembers Ash and gains determination from the memory of his courage. Stepping in front of the others, Goh tells Mew how much of an inspiration it has been to him, even if it doesn't remember their first encounter. Even while Mew charges up and fires a Hyper Beam, Goh stands his ground, thanking Mew for being an inspiration to him. This expression of gratitude catches Mew off-guard, and it dissipates the Hyper Beam before it can hit. It then proceeds to heal all the injured Pokémon, make the rocks glow again, and teleport the Chasers and their Pokémon to the foot of Table Mountain. Despite the sudden ending, Goh is left satisfied by this encounter. When he raises his hand to do his usual "The future's in the palm of my hand" catchphrase, Mew suddenly appears on his palm, much to the shock of everyone present, before it teleports away again, leaving Goh even more enthusiastic and satisfied.
Rain starts to pour down, marking the start of the wet season and the end of the expedition. After sharing their thoughts regarding what they experienced with Professor Amaranth, the team returns to Slateport City. Amaranth declares that the Chasers are disbanded for now, though they are free to reassume that position for the next expedition, with Danika and Quillon already having decided to stay. Goh, Gary, and Horace agree to consider the offer and return to the docks. After sharing encouragements with his friends, Goh parts ways with them and boards a ship back to Kanto. On the way home, he makes a phone call to Ash and asks him how his battle against Leon went.