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Proton is first battled in the Slowpoke Well, where he is leading Team Rocket's plan to cut off Slowpoke tails in order to sell them. He is also encountered during the Team Rocket takeover of the Goldenrod Radio Tower. He is the second of the executives to be battled, after Petrel.
In the original games, a regular grunt is battled in his place at the Slowpoke Well.