The story starts with Blaine restraining Yellow as she cries out for Red, who seems to have been freed from his icy prison. They start discussing what might have happened, as it seems the back of Red was "ripped apart, like it was used for a cocoon". Blaine speculates that someone could have helped him, but seems skeptical to the thought of someone helping Red. Blaine then tells them of how something like this happened during the Silph Co. battle, he reckons it was the same move that did this to Red. Then, someone starts to hack into the signal, Blaine starts panicking that they could have been heard, but it turns out to be Misty. She starts telling Blaine and Yellow that there are some Pokémon armies attacking Pewter City, and that her city (Cerulean City) and Erika's city (Celadon City) have both been destroyed. Blaine tries to tell Brock to get away from his city, but suddenly Misty gets cut off.
Brock races into town with his Geodude, ready to intercept the Pokémon army, as he sees it as his responsibility as the Gym Leader to defend the town. In Pewter City, an army of Machop are tearing up the town, destroying everything and anything in sight, whereas in Cerulean City, Misty is dealing with an army of Gengar. After a futile attempt by her Staryu to fend them off she gets cornered by some, who start to terrorize her. To make matters worse, in Celadon City, Erika is told that an army of ice has taken over three-quarters of the city. Erika tells everyone to do their best to not harm, but tranquilize the enemies. Using her bow and arrow and Vileplume, she starts fending off the invasion of Shellder and Cloyster. She then thinks about who could be behind the armies. Judging from the types she guesses that it must be the Elite Four.
Back in the lab, Blaine too has figured it out, and tells Yellow about an island where the Elite Four are hiding. He tells Yellow they must sneak in and put a stop to the Elite Four, and must do it now, while the Elite Four are occupied with their invasions. Yellow agrees. As they're about to set off Blaine collapses, and tells Yellow to go on without him and to meet up on the island. He hands Yellow the map, and Yellow sets off. Blaine then starts talking about "taking you with me", he then picks up a glove and a Master Ball.
Blaine arrives on Cerise Island, and sees a silhouette, thinking it's Yellow he asks him why he isn't where he should be, but as the shadow draws closer he realizes its Blue and his Golduck. He tells Blue that Yellow will be there shortly, Blue then shushes him, and they hear someone talking in the cave, the voice is talking about how all the Gym Leaders are occupied so it and Yellow will be able to fight. Blaine shouts out to see if anyone is there, then he confronts them calling them "The Elite Four", someone replies, finding it offensive and funny that Blaine would compare them the Elite Four. Blaine then sees three Pokémon: Electabuzz, Muk, and Alakazam. He then sees their Trainers: Koga, Sabrina, and Lt. Surge.
Pokémon are destroying the cities of Kanto while some of Kanto's Gym Leaders are trying to fight them.