Mimikyu first appeared in SM003. When the Team Rocket trio was walking through a forest on Melemele Island, it jumped out of some bushes, scaring them. They initially believed it was a Pikachu. But when the head of its costume fell askew, they were scared yet again, initially thinking the Pikachu's neck was broken. Meowth ascertained that it was not really a Pikachu, but quickly determined that it was creepy, refusing to translate its clicking-type speech. Even Wobbuffet was acutely frightened by Mimikyu. Thinking it was a little cute, Jessie decided to catch Mimikyu anyway. Having no Pokémon yet, since she left Gourgeist in Kanto, she threw Meowth at Mimikyu, commanding him to do Fury Swipes. He connected, but it did no damage due to Mimikyu being a Ghost-type. Meowth continued to be scared of what Mimikyu was saying and demanded it take off its costume to fight him "fair and square" When he tried to unmask Mimikyu, it badly hexed Meowth, suffering a near-death experience. Jessie and James were able to wake Meowth up by dumping buckets of water on him. After relating his near-death experience, Meowth blamed Mimikyu for the hex.
Before they could do anything about it, Team Rocket hid after hearing something approach. It was Ash and his classmates. Upon seeing Mimikyu, the Rotom Pokédex related a story of a researcher having died from shock after trying to peek under a Mimikyu's costume. Having noticed Ash's Pikachu, Mimikyu became enraged. Ash attempted to catch Mimikyu, but Pikachu's Iron Tail had no effect due to its Disguise ability. Mimikyu then beat up Pikachu using Play Rough. Before the battle between Pikachu and Mimikyu went too far, Team Rocket stepped in, determined to catch a Pokémon who was effective against Pikachu. Meowth jumped at Pikachu with Fury Swipes. But when Pikachu tried to counter with Electro Ball on his enemy, Mimikyu intervened and deflected it with Shadow Ball. Speaking through Meowth, Mimikyu told Team Rocket that it would help them against Pikachu, expressing a deep-seated hatred for it. Before it could resume fighting Pikachu, however, a Bewear kidnapped Jessie and James. Meowth was able to get Mimikyu to disengage, and they chased Bewear.
In SM004, Team Rocket and Mimikyu were trapped in Bewear's den. Jessie was attempting to catch Mimikyu with a Poké Ball, because neither Meowth nor Wobbuffet could beat Bewear. But Mimikyu was swatting it away with its tail stick. At some point, James dropped a Luxury Ball he was going to add to his collection. Jessie threw it at Mimikyu, and caught it. At their first battle with Pikachu when Team Rocket was trying to steal a flock of Pikipek along with a Trumbeak and Toucannon that had taken some of Bewear's food, Mimikyu was called out, and used Shadow Ball but after Pikachuused Electro Ball to intercept, Mimikyu used Play Rough on him and was about to use Shadow Claw. But thanks to Rowlet's Leafage, Pikachu was saved. But before the fight lasted too long, Bewear returned and carried Team Rocket away. While a Rowlet had saved the Pikipek, they did get Bewear's food back.