At the Team Rocket HQ, Giovanni decides that they need to use a relatively harmless Pokemon to harness the energy of the Ultimate Pokemon, so that the power doesn't overload and explode, destroying the world. He chooses Jesse's Wabuffet, who they recovered from the Silph Co building. They begin to fuse the Pokemon they have together, using Psychic-Types to borrow the powers of Pokemon around the world to lend to the chimera. Giovanni is so very close to being in control of everything. Just then, the Elite Four appear and challenge Giovanni. They are easily defeated, but are soon joined by Ash and his army. A bloody battle ensues, and many lives are taken. Misty is impaled by a Rhydon, and slowly dies, her blood becoming water that her Pokemon use to gain power. Ash nearly breaks down after Misty's death, but remembers he has to finish things with Giovanni.
The Ultimate Pokemon is almost completely fused. Ash confronts Giovanni himself, and in hand-to-hand combat, they both plunge into the machine that's fusing the Pokemon together. They get caught up in the collective psyche of that Pokemon and are nearly fused together, when May pulls Ash out. Giovanni tries to crawl out, but May jumps in and holds him down. Pikachu plunges in, too, and utilizes the Ultimate Pokemon's brain waves to create a massive electric attack which destroys the machine, but also kills him.
In the aftermath, Ash brings Misty's body to the ocean, laying it into the water. He is approached by the Elite Four to join them and make an Elite Five, but turns them down. He instead returns to Pallet Town, where he first met Pikachu, and trains new Pokemon trainers.