The first Malamar appeared when it took control of Officer Jenny and made her assume the role of Madame X" at an abandoned radio observatory. Soon after, Malamar and Madame X brainwashed a Noivern, a Pangoro, an Exploud, a Scolipede, and a Beedrill. Some time afterwards, Malamar and Madame X came across Jessie, James, and Meowth, trying to figure out how to capture Ash's Pikachu. Malamar overheard them on how strong Pikachu is, and seeks to add Pikachu to its army. Malamar then hypnotized Jessie, James, Jessie's Pumpkaboo, Jessie's Wobbuffet, and James' Inkay then added them to its army. Malamar then attempted to hypnotize Meowth, but Meowth used Fury Swipes on himself to prevent himself from being brainwashed. Meowth then ran off to warn Ash and his friends about Madame X and Malamar, but Malamar commanded the brainwashed Team Rocket to follow him.
After Meowth found Ash and his friends, and warned them about Madame X and Malamar, Malamar, Madame X, and the brainwashed Team Rocket arrived to capture Pikachu. Malamar used Psychic and successfully captured Pikachu. Malamar, along with the brainwashed minions, retreated to the radio observatory. When they return to the hideout, Malamar used Hypnosis on Pikachu and made him a member of its army as well. However, as soon as Malamar completed the hypnotic trance, Ash and his friends, and Meowth found Madame X's hideout and went on a search for Pikachu. As everyone is searching, Malamar cruelly hypnotized Clemont, Bonnie, Dedenne, and Serena. Malamar attempted to hypnotize Ash and Meowth, but Meowth used Fury Swipes on himself and Ash to prevent being brainwashed. Madame X then showed all the powerful Pokémon they successfully hypnotized, as well as commanding Pikachu to attack Ash. While Ash was trying to get through to Pikachu, a machine that Clemont invented early on, that was designed to track down Pikachu's electrical energy, reactivated itself, and rammed right into Malamar. By doing so, all those that were brainwashed by Malamar were freed, including Madame X, who they found out was Officer Jenny.
This unexpected discovery causes the gang to realize that Malamar tricked them into believing that Madame X is a real person and the entire story of her taking over the world was a lie. Malamar then explained that it did all this so it can take over the world. Malamar then retreated to a room where Malamar was making something known as the Ultimate Weapon and Malamar claimed that it will be the beginning of its evil grand design. However, Malamar had no choice but to destroy the weapon as Ash and his friends, Team Rocket, and Officer Jenny saw it, which resulted in the radio observatory falling apart. After the observatory was destroyed, and the others managed to escape, Malamar flies off, making new plans to take over the world.
Some time later, the same evil Malamar from before teamed up with two other evil Malamar and brainwashed the Kalos region's most intelligent scientists to create large energy crystals so they can activate their device similar to the one from the radio observatory in use as a weapon. Afterwards, they stole three delivery trucks and drove up to a mountain called Grace Tower in order to complete their plans. But, when Team Rocket was spying on them due to Inkay causing a ruckus, Malamar ordered its accomplices to search and follow them. They managed to find them along with Officer Jenny, Ash, and his friends. But when they attempted to capture everyone with Psychic, Inkay blinded one of the Malamar with its ink, giving Clemont, James, and Meowth a chance to escape and to get help. However, one of the Malamar followed them to the forest, captured them with Psychic, and blasted off some forest Pokémon with Hyper Beam. Malamar tried to persuade the good Malamar into joining its plans of conquering the world, but the good Malamar and Inkay refused to take part of the action and chased it off with Psycho Cut and Flamethrower.
Meanwhile at Grace Tower, Malamar revealed to Officer Jenny, Jessie, Ash, and his friends the true nature of its plan: to distort the Pokémon world and alternate the environment to suit them. As the plan began to fall into place, Clemont, James, and Meowth arrived in time to rescue their friends with some help from the good Malamar and Inkay they met in the forest. Malamar suddenly grabbed James' Inkay and proceeded in hypnotizing it to attack everyone. But James managed to save Inkay by feeding it a croissant and helped it remember the good times they've had. Inkay then battled the Malamar and managed to defeat them. Officer Jenny disabled the crystal's activation with her Manectric's Thunder and ordered the evil Malamar trio to come with her if they know what's best for them. However they claimed they're heading into the future and swore that they will fight again and their plan will succeed. Soon, the three evil Malamar escaped into the sky with the crystals and destroyed every evidence of their plans, causing everyone to retreat safely from the mountain.
- This Malamar, along with its two other followers, are the only ones of its species that's shown to be evil while other Malamar appeared swimming peacefully with some Water-type Pokémon and living with a group of forest Pokémon.