From Bulbapedia, the community-driven Pokémon encyclopedia.
Project R is an effort put forth by Team Rocket to artificially evolve their Pokémon with radio waves. However, aside from the Red Gyarados, it was unsuccessful, and only caused the Pokémon in the area to become lethargic and appear sick. Short for Project Revolution, it is a revolutionary system that allows Team Rocket to actually manipulate a Pokémon's evolution. Professor Sebastian learned that the evolution-inducing wave can also be used as a great weapon, noting how weakened the group’s Pokémon were in the wave's vicinity. The evolution-inducing waves are meant to make Team Rocket's Pokémon evolve to be stronger and stronger, creating the ultimate Pokémon army. Team Rocket Grunts assist in the project, as do Professor Sebastian and Tyson. The operation is based around the Lake of Rage in Johto.
The operation first appeared in the episode Talkin' 'Bout an Evolution, and reappeared in Rage Of Innocence.