Arriving at Nugget Bridge, Green looks over her Town Map, with Cerulean Cave marked on it as the rumored location of the 150th Pokémon in Kanto. Green looks at the Mewtwonite X and Mewtwonite Y in her possession before using her binoculars to scout ahead. She spots Trace arriving on his Pidgeot and entering the cave after reading a similar report, prompting her to chase after him, but she is quickly accosted by the five Trainers guarding Nugget Bridge with their Pokémon. Unfazed, Green sends out her Gengar and Kangaskhan, taking on all five opponents in a violent brawl, causing the lone Trainer on the other side to watch on in fear as he clutches the prize Nugget. In short order, Green defeats the Trainers and leaves them behind.
Upon entering the cave, Green is briefly beset by a Zubat swarm before catching up to Trace, both of them swearing to be the first to catch Mewtwo and heads deeper into the labyrinthine caverns, not realizing that someone else is watching them. Using her athleticism, Green avoids being cornered by a Graveler and uses her Blastoise to cross a lake, bypassing and defeating a wild pair of Poliwhirl and Poliwrath, allowing her to reach Trace again. In their rush to get ahead, Trace narrowly stops himself from plummeting down a deep crevice, sending out Pidgeot again to fly him over; Green responds by using her Victreebel to latch onto a stalactite and swing herself over as Trace and Pidgeot watch on in surprise. Their surprise is short-lived as another swarm of Zubat and Golbat attack them, prompting Green to order a Razor Leaf to chase the swarm away. Landing on the other side, Trace tends to his Pidgeot's injuries before thanking Green for the save, but also warning her that they're not the only ones pursuing Mewtwo.
Arriving at the center of the caves, Green spots a shadowed figure; thinking that it must be Mewtwo, she flings a Poké Ball at it, only to find that the figure is actually Elaine, who has already caught Mewtwo. Frustrated that her quarry has eluded her, Green challenges Elaine to a battle, sending out her Clefable as Elaine's Pikachu uses Zippy Zap to take Clefable out in one hit. In a jump cut, Elaine faces Green's Ninetales with her Rapidash, but Ninetales's Flamethrower eventually overwhelms it and it falls in defeat. Yelling at Elaine to show her what she came for, Green sends out Blastoise and Mega Evolves it, and Elaine responds in kind. As Mewtwo rises into the air, Mega Blastoise barrages it with a series of Hydro Pump volleys, only to find that Mewtwo has used Protect to shield itself. Using a devastatingly powerful Psychic attack, Mewtwo raises Blastoise into the air and hurls it back into a rock, causing Mega Blastoise to revert; an Aura Sphere defeats Blastoise before Green can reach it. Disappointed, Green recalls Blastoise and acknowledges her loss, offering Elaine the Mega Stones for Mewtwo. To Elaine, Pikachu, and Mewtwo's shock, Green teases them by asking Elaine and Mewtwo to become her Pokémon instead before leaving the scene.
At Professor Oak's Laboratory in Pallet Town, Green reports on her failure to catch Mewtwo and thus complete the Kanto Pokédex, but Professor Oak assures her that she has caught many Pokémon in her quest, and forged strong bonds with her Pokémon in the process. He adds that Green wasn't taking on the initiative alone, pointing out Trace and Elaine standing at the doorway behind them. As Green realizes that her rivals were her allies all along, Oak thanks the Trainers for completing the Pokédex before receiving a call on his cell phone. Speaking to the unseen caller, Professor Oak learns of a brand new Pokémon entirely made out of metal. Delighted, Oak announces to the Trainers that the Pokédex isn't yet complete, but the three Trainers have already left.
Outside, Elaine's Pikachu finds a couple of flowers and offers them to Elaine, causing Green to smile before all three friends walk towards a bright horizon.