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It's a special, almost a film you could say, therefore it doesn't fall in a series,

Pokémon: The Mastermind of Mirage Pokémon, later released in Japan as The Terrifying Mirage Pokémon (戦慄のミラージュポケモン Senritsu no Mirāju Pokemon?) is a special hour-long episode of the Pokémon anime series created for the tenth anniversary of the franchise. It became available on DVD in the United States on September 19 that year as a special feature on the 2-disc Pokémon: Lucario and the Mystery of Mew release (with the Sarah Natochenny version), and the new dub aired on October 28 in the same year on Cartoon Network. In Japan the special was available for download as 戦慄のミラージュポケモン on the official site from October 13-October 31, 2006.

SPOILERS
Here's the plot if you're interested.

Ash is rereading his letter, inviting him to Dr. Yung's lab, to Brock, May, and Max. When he gets there, he is shocked to see Misty and Professor Oak. Dr. Yung appears, and shows them a few mirage Pokémon. He invites Misty to battle one. Misty sends out her Staryu against a mirage Aggron. She is shocked that Staryu's most powerful attacks don't even make it blink. Staryu goes out quickly. Ash begins to battle when an Armaldo suddenly locks up. Yung's Mirage Pokémon System has mysteriously locked up! The controller explodes in his hands, and a handful of legendary Pokémon appear. A stranger, calling himself Mirage Master, uses the system he has just hijacked to his advantage, kidnapping Professor Oak and Dr. Yung. Ash and his friends cannot get back inside because a bunch of mirage Pokémon stand just inside.
Oak, in the custody of Mirage Master, demands to know where Dr. Yung is. Mirage Master ignores his query, and demands the password to Professor Oak's research lab. Oak refuses while a Mew flies in. Professor Oak is greeting it when Mew is attacked. The Professor demands to know why Mirage Master did that. The Mirage Master says that Mew was a failed creation, and he tells Mew to leave.
Ash, Misty, Brock, May, and Max formulate a plan. Ash and Misty will sneak in through the moat, Brock will alert Officer Jenny (with the intention of receiving a candlelight dinner for two), and May and Max will wait in case Ash and Misty get in trouble. They split up. Ash and Misty use Corphish and Staryu to get in.
Team Rocket, after the Mirage System Plans, are looking around. They attempt to burst through a door, only to have it hit them in the noses! Ash and Misty walk through, Team Rocket does the motto, thereby wasting enough time for Mirage Master to check the camera and send in mirage Pokémon. Team Rocket escapes, Ash, Misty, and Pikachu are held by two mirage Machamp and a mirage Ursaring. As the three are being carried, Ash sees Mew appear again, and Pikachu uses Thunderbolt. Some various things are blown up, including a wall, signaling to May and Max. May goes in, and tells Max to wait. Pikachu frees all of them, Misty falls over the edge of the bridge, and Pikachu is recaptured, leaving Ash and Mew. Mew is suddenly trapped by a force field, and Ash manages to get Mew free. Ash discovers that Mew is a mirage Pokémon.
Pikachu is in a fearsome-looking device. Professor Oak asks what the Mirage Master is doing. Mirage Master says he will extract Pokémon data from Pikachu's memory, and that this would not be needed if Oak was cooperative. Pikachu contorts with pain. He looks at the picture displaying Pikachu's memory. Lugia... Entei... Celebi... Latios... Latias... These are all rare Pokémon Pikachu has seen. Oak cannot stand the look of Pikachu, and enters in the password: REDGREEN. Suddenly, Mirage Master has the ability to download information from places around the world. Tracey and Professors Elm and Birch stare at computers in their labs, while Nurse Joy deals with problems at the Pokémon Center.
"You have to believe me, Officer!" Brock pleads to Officer Jenny. "We need to go to Professor Yung's lab for a candlelight dinner... I mean-" Nurse Joy flickers onto the officer's computer. She tells the officer that someone is downloading massive amounts of Pokémon data. Brock tells her about Mirage Master, and they leave.
Misty is hanging onto the edge of a bridge. She suddenly loses her grip, and May appears in the nick of time to save her. They go upstairs. Ash and Mew are there already, and the process of creating the Pokémon finishes in a flash of light. A mirage Mewtwo emerges. He attacks them, and they run. Outside of the boundaries of the Mirage System, the heroes think they are safe. Then, missiles are launched from the towers, and they expand the system! Mewtwo and Mirage Master emerge. Mirage Entei, Articuno, and Zapdos suddenly appear. Oak correctly guesses the identity of the Mirage Master. Mirage Master removes his mask, revealing Dr. Yung! Oak reveals that when Mirage Master first appeared, he was a hologram, and that Yung was expelled from the Pokémon Institute for his research, deemed disrespectful to Pokémon. Yung's Mewtwo and Ash and company battle. Yung is about to obliterate Pikachu when Mew takes the blow. Mew then is absorbed into the Mirage System. Yung says "good riddance," and Mewtwo absorbs the entire Mirage System database. Ash is enraged that Mew is called a failed creation, and the attack begins anew.
Team Rocket is blown away in this fight. Pikachu is about to be killed when Mew holds Mewtwo back! Ash orders Pikachu to perform Volt Tackle, and Mewtwo is destroyed, as are Mew and the System. The fortress is now aflame, and Yung retreats inside. The police are searching, as are firefighters, but they cannot find him yet. The gang discusses what happened, and agree that Mew was far more than just data and certainly not a 'flawed specimen' as Yung believed.

Sources:
https://en.wikipedia.org/wiki/Pokémon:_The_Mastermind_of_Mirage_Pokémon
http://bulbapedia.bulbagarden.net/wiki/The_Mastermind_of_Mirage_Pokémon

Hope I helped!

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