Be prepared! Mewtwo is a level 70 Pokémon, and it knows Psychic, Aura Sphere, Barrier (raises its Defense), and Recover (restores half its HP). You will need Pokémon stronger than Mewtwo. Get a Pokémon that can Paralyze it, a Pokémon that knows Sing, or any other Pokémon that uses any other status condition. In this type of battle, you need more strategy than power. Do not use Toxic, Will O' Wisp, or any move that causes a HP-sapping status condition. This makes damage worsen every turn, and Mewtwo is going to faint quickly if you are not careful. When you are ready, advance. Paralysis is best, since this condition makes Mewtwo slower, easier to catch, and less likely to use moves.
Defeat the Elite Four. You will need to beat the Elite Four and complete the main game before you can get Mewtwo. See this guide for details on how to best build your team to take down the Elite Four.
Stock up on Poké Balls for the battle. Mewtwo is a tough catch, and you will need a large number of Ultra Balls, Timer Balls, Dusk Balls, and/or a Master Ball (if you still have it).
Understand the catch rate of the balls. The Ultra Ball is ineffective, but 40 may work (this is not, however, guaranteed). Timer Balls are if there at least 30 turns. The Master Ball always works, unless you are trying to catch a trainer's Pokémon-but you may need it later.
Build your party. Mewtwo is level 70, which means you're going to be in for a tough battle. Make sure that you have a party that can survive Mewtwo's attacks as well as put out enough damage to lower its health for capturing.
Travel to the Pokémon Village. You can find Mewtwo outside of Pokémon Village. Pokémon Village can only be accessed by traveling down Route 20 in Kalos.
Find the cave on the edge of the village. Walk to the left after reaching the village until you reach the edge of the river. Use Surf and travel up the river until you reach the waterfall. Jump back onto the ground on the right side of the bottom of the waterfall. Walk down the path to the right until you reach the cave. The cave entrance will be blocked until you become the Champion, by defeating Diantha.
Save your game. Once you enter the cave, save your game. If you accidentally make it faint you can refresh. Don't worry if you leave before talking to it: It's going to stay there unless it's in a battle.
Talk to Mewtwo. After saving and ensuring that everyone is ready, walk up to Mewtwo and talk to it. After a short cut-scene, the battle will begin! If you are going to use any pokéball other than a Master Ball, go ahead and dwindle its HP down.
Aura Sphere deals 80 damage to your team and it never misses. Psychic deals 90 damage (unless you have a Dark-type Pokémon). Barrier sharply raises its defense. Recover restores half its HP. One strategy is to make it waste all it moves or, give it the asleep or frozen status condition.
Start throwing Poké Balls. Now that Mewtwo is nearly defeated, it's time to start chucking Poké Balls at it. Ultra Balls aren't guaranteed to work, so you'll likely have to throw quite a few before you can capture Mewtwo. If it heals himself, use your Pokémon to lower its health again before throwing more balls.
Mewtwo will be caught when the thrown Poké Ball shakes 3 times and turns dark in color. Mewtwo is going to be a strong addition to your party when caught! You can only get one in the game, so be careful not to release this creature.
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