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Team Rocket's map of Lake Rage, used during the project
Project R, short for Project Revolution, is a Team Rocket operation to artificially evolve their Pokémon with evolution-inducing waves. The operation is based around the Lake of Rage in Johto.
In the anime
Ash and his friends accidentally stumbled onto Project R in Talkin' 'Bout an Evolution while making their way towards Mahogany Town. Professor Sebastian was revealed to be the mastermind behind the entire operation, while Tyson managed the Team Rocket Grunts and mitigated any threats. Lance infiltrated the Team Rocket research facility in disguise and learned more of Team Rocket's intentions.
The operation was intended to make Team Rocket's Pokémon evolve to be stronger, creating the ultimate Pokémon army. However, it only led a Lake of Rage Magikarp to evolve into a Red Gyarados. Team Rocket later retrieved the Red Gyarados in the hopes of studying it further to perfect their technology. Professor Sebastian also learned that the evolution-inducing waves caused the Pokémon in the area, including Ash's Pikachu, to become lethargic and appear sick.
The operation was ultimately thwarted in Rage Of Innocence by Lance and his Dragonite. Officer Jenny made several arrests, including Tyson, though Professor Sebastian had already fled the scene in a helicopter. Lance also went on to catch the Red Gyarados.