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Meloetta was first pursued by Team Rocket in Virbank City. It was able to elude them but somehow made its way into the Pokéstar Studios where Ash had encountered it. After he saved it from a collapse of the falling billboards it stayed close behind him, following him to Virbank Gym.
Meloetta appeared again in All for the Love of Meloetta! where its invisibility form was compromise by Team Rocket when they used their anti-stealth goggles created by Dr. Zager to see through her invisibility. Then Jessie calls out Woobat while James calls out Yamask and attack it with Air Slash and Shadow Ball to force it out of hiding from the bushes, respectively. Meowth then tried to catch it by firing an electric net but it was able to make its escape. However, it was injured in the process, fell off the cliff, and wandered into the street in a daze, almost getting run over by Cynthia's vehicle. Ash was able to recognize Meloetta from before and Cynthia applied potion to its wounds. Then they attempted to get its fever down with a bag of ice. While Iris and Cilan searched for an Oran Berry for it, Ash kept watch.
After a little bit Oshawott came out of his Poké Ball, sensing Meloetta's presence, and instantly develops a very major crush on it upon sight. Meloetta recovered a bit after eating an Oran Berry Emolga brought although it lost control from the gust of wind and hit Oshawott's head causing both of them to be knocked out. During this time both Emolga and Oshawott were arguing with each other when both of their heads are hurt and Meloetta began to sing in order to calm them down. Afterwards, it disappeared once more but it had followed Ash and the others to Cynthia's Villa in Undella Town by boarding the seaplane while Team Rocket discovers her presence that Meloetta was following Ash and co. So they go to Undella Town before Ash and co. arrives at the Undella Town seaport.
In Piplup, Pansage and a Meeting of the Times!, it followed Ash and snuck into Jervis's car and headed straight to Cynthia's Vacation Home while Team Rocket quietly follows them by their truck. When Ash sees a Rattata, Meloetta appears and sits on Ash's lap. Seeing Ash, Meloetta seems very excited, when Cynthia says that Meloetta must really like Ash. A while later, they arrive at Cynthia's villa, but when Jervis opens the door, Meloetta suddenly disappears again. A while later, when Ash and co. let their Pokémon see their old friends Dawn and Piplup, and her Pokémon, Meloetta secretly comes. The Pokémon can sense Meloetta, and Ash knows it's nearby and calls it out to meet Dawn. Meloetta appears and Dawn get acquainted. Upon seeing Meloetta, Dawn's Piplup instantly develops a huge crush on it, just as Ash's Oshawott before it. Oshawott attacked him with Aqua Jet, upset to see Piplup and Meloetta getting along, sparking a rivalry. During the battle between Dawn's Piplup and Cilan's Pansage, Meloetta was excited about the battle way it was in a Pokémon Contest and was happy for Piplup. Then Team Rocket made their decision to give Meloetta a little more time to spend with Ash and co. long enough and record the whole song of Meloetta by sunset and report to Dr. Zager in the submarine. But then, Dr. Zager thinks the whole song was not enough if they leave them all together long enough. And now they let Ash and co. to take care of Meloetta's work for Team Rocket while they find the ruins of the Abyssal Temple.
In Expedition to Onix Island!, Team Rocket appears and on the move again dropping sensors around the ocean in their helicopter in order to cover the whole ocean floor to find the ruins of the Abyssal Temple while Meloetta spends her time with Ash and co. on their expedition on Onix Island to find the special Onix. After they drop every sensors around the ocean, they say they words that they'll find the ruins for sure and grab every data they could on Meloetta, let Ash and co. take care of Meloetta's work for them, and do it all for the boss.
In The Mystery of the Missing Cubchoo!, Team Rocket were in their submarine again and submerged deep to the ocean floor when one of their sensors picked up something. By then, when they're way deep enough on the ocean floor, they turn the submarine's light on and monitor on to view the screen and they've found the ruins what they've been looking for and send the image to Dr. Zager on what they've discover.
In the end of Iris and the Rogue Dragonite!, Team Rocket appear once more and still in their submarine researching the entire map of the ruins around a bit more in order to get the whole map. Until Goodbye, Junior Cup - Hello Adventure! after the World Tournament Junior Cup, they've uncover the location of the Abyssal Temple.
In Meloetta and the Undersea Temple! and Unova's Survival Crisis!, Giovanni returned to spearhead Team Rocket's: Operation Tempest, a stratagem which involved capturing Meloetta. He did just this using goggles created by Dr. Zager to be see the mythical Pokémon even when she was invisible. Giovanni quickly defeats Ash and rejoins Jessie, James, Meowth and Zager. Team Rocket led Giovanni to the Abyssal Temple which they had spent a while looking for. With Ash & Pikachu captured, Giovanni uses Meloetta to summon the Reveal Glass and rise the Abyssal Temple, using Meloetta's Calming Song, that Team Rocket had insidiously recorded during her time with Ash. Meloetta is caused to suffer in this ceremony. The Kami trio are summoned and the Reveal Glass morphs them into their, feral, vicious Therian Formes. At Giovanni's command, they battle the resistance created by the escaped Ash, Pikachu and their friends, Iris' Dragonite leds this resistance. In the midst of a titanic battle, Ash and Pikachu confront Giovanni. Ash orders Pikachu use Electro Ball, because Pikachu had been charged up from an earlier attack, the Electro Ball's size and power are augmented significantly. The electric attack incinerates the platform Giovanni was standing on and severs the link between the sadistic leader and the tortured Meloetta. However Giovanni loses his mind because of this ordering the Kami trio to destroy the Unova region. Jessie, James and Meowth throw themselves at their beloved boss and successfully save him, not only from a fatal explosion but from his insane state. Team Rocket then make a total retreat to Kanto.
Ridley takes control of the Reveal Glass and with Meloetta's Calming Song, calm the Kami trio, revert them back to their Incarnate Formes and back to where they belong. Ridley as Meloetta's guardian leaves with her after a final goodbye to Ash and friends and bids her farewell.
Meloetta also appeared in the Pikachu Short titled, Meloetta's Moonlight Serenade.
- Meloetta is revealed to have the ability through her song to summon the Abyssal Ruins and the Reveal Glass to turn Tornadus, Thundurus, and Landorus into their Therian formes.