After going through Victory Road, Red makes it to Indigo Plateau, where he fights against the Elite Four. He defeats Lance, who tells Red that he can be Champion if he completes one more challenge. Red is surprised that the Champion is Blue, who is also surprised that Red made it. While Red was battling, Blue was busy searching for the right Pokémon to match up with his opponents. The battle begins and after some intense fighting between both Trainers' entire teams, when Blue's Blastoise defeats Jolteon, Red sends out his final Pokémon, Charizard. Blue remarks that this is similar to Red and Blue's first Pokémon battle, and he taunts Red by saying he (Blue) won. Red counters that the tables have turned. And with that, the two Pokémon fight each other. Blastoise uses Hydro Pump and nearly beats Charizard, but Charizard holds on and uses Fire Spin to knock out Blastoise. Blue begins to ponder why he lost, and declares Red the Pokémon Champion.
Professor Oak makes a visit and congratulates Red on his victory, and reprimands Blue on his loss, saying that he didn't treat his Pokémon with love. Oak takes Red to the Pokémon Hall of Fame, where Red is put in a picture with his six Pokémon. Red's journey is not over yet; he still works to complete his Pokédex, catching the remaining Pokémon he had not yet caught.
Later, having captured all of the remaining known Pokémon in the region, including the legendary Articuno, Zapdos, and Moltres, he triumphantly returns to Pallet Town, only to find the lab empty. He looks for Professor Oak, and one of his aides tells him some serious news. Blue was severely injured while exploring Cerulean Cave, when he had encountered a Pokémon never seen before. Blue's Pokémon were no match, and Blue himself was crushed by his Blastoise, who had been thrown at him by this adversary's attack. When asked if the Pokédex collected any data on this mysterious Pokémon, Blue reveals that his Pokédex was inadvertantly crushed by Blastoise during the encounter. Red and Professor Oak try searching for the Pokémon in Red's Pokédex, even narrowing it down to a Psychic-type Pokémon, but Blue confirms that nothing in the Pokédex matches this Pokémon. Blue tries to stop Red from suffering the same fate as him, and that causes Red to remember some of what he had from a book in the Pokémon Mansion. Meanwhile, in Lavender Town, Mr. Fuji hears rumors of a viciously powerful Pokémon in Cerulean Cave, and fears the worst. He has seen it before, back in his glory days. Red remembers some diary entries of the book. Oak was surprised that Fuji gave Red the gems. Red tells Oak about the diary entries, and Oak tells that Fuji was Professor Fuji before his studies were halted. He suggests that Red needs to keep the stones, one for Charizard, and one for him.
Back in Lavender Town, Mr. Fuji gets word that Red has gone to Cerulean Cave. He fears Red is going to challenge the monster he discovered long ago. There is all but a small chance of winning ever since he met him at the Pokémon Tower. Fuji remembers a legend from the Kalos region, that if a trainer and his Pokémon have a strong friendship, the Pokémon can transcend normal evolution. Meanwhile, in Cerulean Cave, Red battles Mewtwo, but none of his Pokémon have any effect; even Articuno is easily defeated. Eventually, he sends out Charizard, and after the two Pokémon fight for a bit, Red tries to catch Mewtwo in an Ultra Ball, but Mewtwo easily breaks out. Charizard continues fighting, with Red even risking himself to save his Pokémon, but Mewtwo sends Charizard and Red into the water, leaving them to drown. All of a sudden, Charizard begins to glow, and so do Red's stones, which turn out to be Mega Stones. This causes Charizard to Mega Evolve into Mega Charizard X. With its newfound power, Charizard goes on the offensive, finally slamming Mewtwo into a nearby stalagmite with a Mega Punch, weakening it enough for Red to catch it in another Ultra Ball. After catching Mewtwo, he celebrates with Charizard for finally completing the Pokédex. Back in Pallet Town, Professor Oak and the boys eat lunch, Blue complaining that he should have been the one to catch Mewtwo, but then Red remembers what the diaries said about Mewtwo coming from Mew. He decides to find it and catch it. Right outside the window, a Mew comes into view before flying away, as if teasing Red.
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