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The story begins with Ash and his friends walking through a forest. Ash proudly reads a letter he recieved from someone named Dr. Yung inviting him to witness the unveiling of a new battle system. May, Max and Brock seem rather exasperated as Ash brags on.

Soon the group reaches Dr. Yung's laboratory castle. As they enter they observe many black domes on the ground, which Brock assumes to be an outdoor lighting system, then they bump into two old friends---Misty and Prof. Oak, who had also been invited by Dr. Yung. Oak tells the group that he believes Yung's years of research have come to an end, a fact confirmed by the doctor himself as he steps into the courtyard.

After a round of introductions, Ash asks Yung to show him the battle system. Yung surprises them by saying they are inside of it, then he takes out a remote control and taps some keys on it. The black domes open up to reveal crystal generators, and in turn the generators form a force field on the ground. Oak recognizes this as a Mirage Field, then Dr. Yung summons a Kabutops, an Omastar, and an Armaldo from the generators. Prof. Oak calls these three "Mirage Pokémon" and tells Yung that the Mirage System must be completed, a fact Yung confirms. Yung tells of how his Mirage System can create any Pokémon complete with voice, intelligence, and attacks all from their data. He continues on to say that the system can create any Pokémon despite its rarity or even its being extinct. When he is done boasting, Yung erases the fossil Pokémon, reforms them into a Mirage Aggron, then challenges Ash and Misty to a battle. Ash is ready to face Yung, but Misty stops him and says ladies first, so she is the first to battle. Meanwhile, Team Rocket has been eavesdropping from the other side of the gate and hatch a plan to steal the Mirage System.

Elsewhere in Yung's castle, he and Misty are about to battle. Misty sends out her Staryu and orders it to attack Aggron with Bubblebeam. The attack hits, but Aggron isn't fazed at all. Yung commands a Sandstorm, which Staryu tries to dodge---but the blast curves upward and hits it hard anyway. Brock and Ash comment on how tough Mirage Pokémon are, but noone other than Pikachu notices a Mew watching the battle from atop one of the castle's walls. Misty tries having Staryu use Water Gun, but Aggron dodges, uses Thunder Wave to paralyze Staryu, then finishes it off with Bullet Seed. Misty recalls Staryu in shock, and Max comments that Aggron shouldn't be able to use Thunder Wave or Bullet Seed. Dr. Yung explains that because it is a Mirage Pokémon, Aggron can use any attack simply by changing the data written into it.

Ash now faces Aggron. As Pikachu and Aggron charge towards each other, however, Aggron begins to 'glitch.' Oak asks Yung what's the matter, but Yung doesn't know. He frantically presses the buttons on the controller, but it explodes and knocks him down. Aggron is deleted back into the generators as Oak rushes to Yung and helps him up. Suddenly, however, the Mirage System suddenly activates and the fossil Pokémon return, along with a pair of Aerodactyl. Yung doesn't understand what is happening or how the system could work without the controller, but a sinister laugh floats over the area. Up on the castle balcony, behind the Mirage Pokémon, stands a masked man wearing a black cowboy hat and a black cape. He calls himself 'Mirage Master,' then orders the Mirage Pokémon to attack. One of the Aerodactyl dodges Pikachu's Thunderbolt, captures Dr. Yung, and flies off to the balcony with him. The others nearly escape, but before they can, Mirage Master pulls out a second Mirage System controller and uses it to make Armaldo fire a Shadow Ball. The attack makes Max fall, and Oak rushes back to help him. Ash, Brock, Max, May and Misty escape through the gate and the fossil Pokémon vanish (they cannot move outside the Mirage System's field) but the second Aerodactyl captures Oak. Ash is about to go back in, but Mirage Master regenerates the fossil Pokémon to block the entrance.

Up in the tower, Oak is held captive surrounded by a Mirage Houndoom, a Mirage Absol, a Mirage Machoke, a Mirage Machamp, a Mirage Mightyena, and a Mirage Ursaring. Mirage Master appears and welcomes him to Dr. Yung's lab, but Oak just shouts at him to tell what he did to the doctor. Mirage Master laughs and brushes off the demand, then commands Oak to give up the password for his research lab's database...a command that Oak flatly refuses. Without notice, Mew flies in and hides behind Ursaring as Mirage Master threatens Oak. Oak still refuses, and pulls a Poké Ball from his pocket. Mightyena snarls and stops him, however. Mirage Master boasts that no Pokémon can stop his Mirage Pokémon.

Outside the castle, Ash and his friends are hatching a plan to get in and save Oak and Yung. The first part entails going to fetch Officer Jenny to report the kidnappings, so of course, Brock volunteers to go and rushes off. Ash and Misty then decide they'll be the ones to go in while May and Max wait outside for Jenny. They agree, but promise to come running if something goes wrong.

Meanwhile, Mirage Master describes his plan to Oak. He believes Pokémon are 'weak' and 'incomplete,' and plans to use the Mirage System to create a Pokémon with absolutely no weaknesses. Oak screams at him, saying that something like that would throw off the balance of nature. However, Mirage Master just brushes him off again and presses a button on his giant computer keyboard, activating a glowing booth next to him.

Using Corphish and Staryu, Ash and Misty swim into an open hole in the side of the castle's basement. They discover that the Mirage System generators are inside, as well, and decide to move ahead cautiously. Elsewhere in the basement is Team Rocket, looking for the Mirage System design plans. They find a door and are about to go through it when it opens and slams them in the faces. They then find themselves face-to-face with Ash and Misty. Mirage Master can see this through a security camera, and sends the Mirage Pokémon in the lab after them. When Ursaring fades he sees Mew, becomes enraged, then attacks it with a Mirage Magnemite. He tells Oak that Mew is a 'flawed specimen,' and commands Mew to get out of his sight. Mew sadly leaves.

As soon as Team Rocket finishes their motto, the Mirage Pokémon appear. They put their hands up in fright, but when Houndoom snarls at them, they scream at it. Houndoom then blasts them off with a Flamethrower. Having no choice but to fight, Ash sends out Pikachu. He and Misty then see Mew appear, but this distraction allows Mightyena, Absol, and Houndoom the chance to attack. Ash orders a Thunderbolt, but Absol dodges and Headbutts Pikachu into the wall. Misty tries to send out Staryu, but Machoke grabs her. The same thing happens to Ash, Machamp grabbing him when he tries to call out Corphish. Finally, Pikachu is grabbed by Ursaring, and all the Mirage Pokémon begin to march back to Mirage Master. Mew follows them.

While the Mirage Pokémon are carrying them up a long, spiraling network of platforms, Ash tells Pikachu to Thunderbolt Ursaring and escape to May for help. Pikachu tries, but the attack doesn't harm Ursaring at all. Ash tells it to try harder, so it does. This one knocks down Ursaring and sends a lightning bolt blasting out the side of the castle. May and Max see it and realize something's gone wrong, so May sends out Squirtle and begins to swim towards them. Meanwhile, Pikachu fires more Thunderbolts, knocking out the crystal generator nearby. Its next attack knocks Machoke and Machamp back, and Machoke drops Misty into the pit. This distracts Pikachu, who is then knocked out by another Headbutt. Ash tries to run to it, but Machamp tackles him and knocks him out as well. The Mirage Pokémon then pick up Pikachu and march off again. Mew shakes Ash to wake him up, and Ash returns the favor by pushing Mew out of the way of some falling rocks. Ash finds out that Mew is also a Mirage Pokémon despite its different demeanor. Mew then lands on the broken crystal generator, and a red force field surrounds it. Ash manages to push through it and pull Mew out, then he calls down the pit to Misty with no answer. Mew tells Ash to follow it, so he does. Misty, meanwhile, is hanging off the side of one of the platforms. The brick she's holding slips, but before she falls May appears with Squirtle and saves her.

Up in the tower, Mirage Master hooks Pikachu up to some sort of machine. He explains to Oak that he is going to extract Pokémon data from Pikachu's memory because Oak would not give up the password. He activates the machine with the press of a button, and Pikachu's memories begin to appear on the screen. Lugia, Entei, Celebi, Latios and Latias all appear on the screen as Pikachu screams in pain. Oak finally stops him and decides to give up the password, so Mirage Master lets Pikachu go. Oak types the password "REDGREEN" into the computer, then Mirage Master downloads all of Oak's research data onto his own computer. He then begins cracking databases around the world, at Pokémon Centers and at the labs of Prof. Elm and Prof. Birch. With all this data, Mirage Master announces he can now create the ultimate Pokémon. A glowing orb of electricity appears in the booth next to the computer.

At the police station, Brock yells that Jenny needs to get over to Yung's lab right away. He slips and says it's for a candelight dinner before mentioning something terrible has happened, but then Nurse Joy appears and tells Jenny that massive amounts of data are being downloaded from Pokémon Centers worldwide.

Oak and Mirage Master look on as the orb gets bigger and brighter, but then a familiar cry comes. It's Mew, with Ash following close behind. Ash takes Pikachu from Oak, then wonders what the glowing orb is. Mirage Master announces it is time for the ultimate Pokémon to be born, and screams out for Mewtwo to awaken. The force from the machine blows out the windows (something Max spots from outside) May and Misty arrive at the lab just in time to see Mew before the bright light fades and a sinister shadow appears in the booth. It's a Mewtwo, but as Mirage Master explains, no ordinary Mewtwo. It is a Mirage Pokémon able to use any attack, he explains, then orders it to demonstrate. With one Shadow Ball, Mewtwo destroys all the Mirage Pokémon. Mirage Master then orders it to attack Ash and his friends, but Prof. Oak sends out a Dragonite and uses Twister to deflect Mewtwo's Shadow Ball. They all then flee, with Mew following.

The group meets up with Max at the front gate of the lab. He sees Mew, but can't look at it for long. The towers of the castle open up, and begin firing hundreds of missiles into the air. Oak realizes what they are in horror. When the missiles hit the ground, they open up and activate portable Mirage System crystal generators---allowing the Mirage Pokémon a massive range of attack. Mirage Master appears with Mewtwo and announces he will use the system to take over the world, then he summons a Mirage Entei, a Mirage Articuno and a Mirage Zapdos. Team Rocket appears in a nearby bush and decides to try and capture the Mirage Pokémon. Mirage Master says that this is the culmination of his long years of hard work, something that makes Oak stop dead in his tracks. Oak tells Mirage Master to stop...then suddenly addresses him, to the shock of all, as Dr. Yung!

Max says that the Aerodactyl carried Yung away, but Oak explains that the first Mirage Master appearance was a mirage itself and the kidnapping was a fake so Yung could execute his plan. Mirage Master laughs and takes off his hat and mask, revealing that he is indeed Dr. Yung. Oak explains that he knew it was Yung by how he reacted to Mew and how he referenced 'many years of hard work.' Yung says he wants revenge for being kicked out of the Pokémon Institute, and orders his Mirage Pokémon to attack. Misty sends out Gyarados and May sends out Combusken, then Entei uses Flamethrower. Ash tells Pikachu to use Iron Tail, but the Flamethrower knocks it down. Gyarados and Combusken try Hydro Pump and Fire Spin, however they are dodged and hit by Articuno and Zapdos. Oak then orders Dragonite to use Hyper Beam...on Mewtwo. It fires the beam, but Mewtwo simply puts up its hand and catches the attack. Next, Mewtwo flies up and punches Dragonite square in the face, then smashes it down to the ground with its tail. Mewtwo then floats back down as Yung brags that normal Pokémon cannot defeat his Mirage Pokémon. Mewtwo puts its hand up...then its hand congeals and forms the head of an Arcanine! Yung bids Oak farewell, then Mewtwo launches a massive Flamethrower from the Arcanine head straight at him. Pikachu jumps in the way and shocks the fire, but still takes the hit. Yung decides he'll kill Pikachu instead, and orders a Hyper Beam. Mewtwo's hand congeals again, this time into a Rayquaza head, and the beam is launched...

After the explosion from the impact clears, Ash sees that Pikachu wasn't hit! Mew had gotten in the way and put up a shield to protect Pikachu. Furious, Yung orders Mewtwo to attack. Mewtwo rushes forward and slams Mew into the ground with its tail, uppercuts it into the sky, then congeals both its hands into Tropius heads and fires two massive Solarbeams. Mew takes catastrophic damage from Mewtwo's barrage, and is deleted. Yung smugly tells good riddance to the flawed specimen, but this only angers Ash. Yung stays calm, however, and pulls out his strongest weapon yet---he erases Entei, Articuno and Zapdos, writes them into Mewtwo, then writes all the data in the Mirage System into Mewtwo as well. Mewtwo screams, and heads of various Pokémon begin popping out of its body. It then fires off a Hydro Pump, a Flamethrower, a Thunderbolt, a Bullet Seed, a Hyper Beam and other attacks. Ash orders a Thunderbolt from Pikachu, Misty a Hydro Pump from Gyarados, May a Fire Spin, and Oak a Dragon Rage. The attacks collide in an explosion...and Mewtwo's win out, knocking all of the Pokémon down. Gyarados almost crushes Team Rocket, but they only end up being blasted off.

Ash tells Pikachu to keep fighting, and despite how much it's taken, it does. Yung tells him to give up, but Ash says he's fighting for Mew and orders a Quick Attack. Yung also tells Mewtwo to use Quick Attack, and Mewtwo headbutts Pikachu all the way back to where it started. Mewtwo then floats over and stands over Pikachu as Yung commands the finishing blow: Mega Punch. Mewtwo winds up and swings its fist towards Pikachu but suddenly stops as if it is being held back. A red aura surrounds it, and from this aura appears Mew, who is using its powers to hold Mewtwo back. Yung, even more furious, presses the buttons on his controller in an attempt to power up Mewtwo even more, but the system overloads and jams. Oak tells Ash that their only hope for success is to attack Mewtwo while Mew is holding it back, even though doing so would destroy Mew as well. With tears in his eyes, Ash can't bring himself to order an attack...until Mewtwo begins to turn around and break Mew's hold. Ash finally decides it has to be done, and orders Pikachu to use Volt Tackle. Pikachu nails Mewtwo square in the chest and it explodes, erasing Mewtwo. Mew then slowly deletes as well, as its friends look on sadly. The Mirage System crystal generators begin to explode, and soon the whole castle is in flames.

Oak tells Yung that it's over, and orders him to go along with him and the others. Yung refuses and instead goes back into his burning castle, and rubble falls to block the entrance. That evening, Officer Jenny tells Oak that they can't find Yung anywhere. Misty and Ash comment on how kind Mew was, and promise to one day meet it again.

Thanks to TheGreatButler for writing this for us