An explosion occurs in a Team Rocket laboratory and Mewtwo escapes to Blaine's horror as it explodes out the side of the building. Waking up in a sweat next to his Rapidash, he realizes it was just a nightmare. Feeling pain in his right arm, the scientist looks towards Cerulean City's northwestern sector, before continuing on his way on Rapidash's back.
At the Pokémon Center, Red is informed by Bill of a "beast" that had attacked the northwest sector of Cerulean City, razing it to the ground, before disappearing into Cerulean Cave. He sternly warns him that his confidence from helping take down Team Rocket should not let him think he's capable of capturing such a Pokémon. Red nervously laughs to himself as he exits the Pokémon Center, Bill's warning coming a bit too late when he's already there.
Walking through the destroyed landscape with his Pokémon, he's amazed at the extent of the devastation, his expectations of it as a powerful Pokémon far surpassed. Suddenly coming across a cave entrance, his Pokémon nervously stand back, refusing to enter. A tornado suddenly emerges out of the mouth of the cave, sweeping up Red and his Pokémon. Thinking quickly, he has all his Pokémon cling together in a long chain, with Aero on top trying to lift them out. Aero straining under the combined weight, he reaches for his Poké Balls to recall his other Pokémon, but they're missing, presumably blown away. Barely lifted out over the top of the tornado's tunnel, Aero's grip falters, leaving them all to fall back down.
Suddenly a hand grips onto Red, giving him a handful of Poké Balls, which he quickly uses to rescue his Pokémon. The stranger reveals himself to be Blaine, having pulled Red on top of his Rapidash. He explains that the tornado is being caused by the Pokémon Red was seeking out, and says he can leave if he likes, but he needs to fight to stop it. Commanding Rapidash to use Fire Spin, the attack is bounced back after striking the side of the tornado. Blaine tells Red that the tornado is actually being caused by extremely powerful Psychic abilities, Psywave able to create a cyclone of pure energy that functions as a shield that reflects back any attack, creating both a strong defense and offense at the same time. The Pokémon command the Psywave is at the very base of the tower of swirling energy, only one Pokémon in the world capable of such immense power.
Mewtwo rises to attack them, quickly vanishing and appearing behind them, as the skin on Blaine's arm begins to slide down, as if melting. They narrowly avoid an attack, and Red comments on Blaine's arm in horror as his condition seems to worsen. Blaine stares at his arm, and says this is the reason that Mewtwo needs to be defeated. He reminds Red of Mewtwo's history as the Pokémon he helped create using one of Mew's cells, but begins to elaborate. It's not possible to create an entire new Pokémon from the small sample of Mew cells they had, so Blaine added some of his own cells from his arm to the process. Mewtwo's cells still lurking in the syringe he used, they managed to infiltrate Blaine's body, and are now beginning to take control of his him, which will culminate in the end of his life.
Blaine laughs and says the one benefit to the situation is that it allows the both of them to know when the other is nearby, essentially allowing him to function as a Mewtwo locator as long as he's still alive. He has Rapidash envelop Red inside a ball of fire, keeping him safe inside, not wanting to drag him into his confrontation with Mewtwo. Red protests, but Blaine refuses his help, emphasizing that this isn't just another adventure, and city after city will be destroyed if he doesn't act now. He pats Red on the head, commenting that one day he'll be a powerful Trainer, before he rushes towards the bottom of the tornado on Rapidash to confront Mewtwo.
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