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i accidentally used my masterball on moltres so I was looking for tips on catching mewtwo without one.

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Here are some tips:

1: Get his HP into the red.
You already knew this, but keep in mind that Mewtwo knows Recover. False Swipe is the best move to get his HP to the lowest possible point.

2: Give him a status effect.
Pokémon with a major status condition are easier to catch. I suggest paralyzing it with Thunder Wave. Paralysis is the best because Sleep isn't permanent, and Burn and Poison might KO him.

3: The right Poké Balls.
Ultra Balls and Dusk Balls will have the highest catch rate. You can also throw a Quick Ball on the first turn and hope for the best, or pile up on Timer Balls — after 10 turns have passed their catch rate goes up.

4: Bring healing items.
Mewtwo is one tough cookie so pile up on Max Revives and Hyper Potions.

5: Save before attampting capture.
This way, if you accidentally KO Mewtwo you can just reload your save and try again.

6: Pick the right Pokémon.
Assuming this is in XY, I suggest Aegislash. It's bulky enough to tank Psychic in Shield form, is immune to Aura Sphere, and learns False Swipe. Make sure it knows King's Shield to get back in Shield Form, Swords Dance because Mewtwo likes to raise its defense with Barrier, and of course False Swipe. Maybe Shadow Sneak as well to knock off chunks of HP early on.

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this is great, but what would be the right pokemon in blue? (thats the game im trying to catch him in.)
Yeah, most of it will still apply. Only changes are:
• Mewtwo will know Swift instead of Aura Sphere.
• There are no Timer, Quick or Dusk Balls.
• Obviously there is no Aegislash ;)

EDIT: Oh you're asking for what Pokémon to use. Totally misread that. I'll look it up.
Okay, so it turns out False Swipe wasn't around until Gen 2. I suppose you'll just want something bulky that can Paralyze Mewtwo. If it's not too hard, Zapdos would be a good choice — it's bulky and with TMs you can teach it Rest for recovery and Thunder Wave, plus it has strong moves like Thunderbolt to lower Mewtwo's HP.
I got him thanks!!!!!
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What I am about to tell you applies with any Pokémon.

When attempting to catch a Pokémon, always try to make its health as low as Possible. Carrying a Pokémon with the move False Swipe is highly advised, since it will prevent a Pokémon from fainting, leaving it with 1 HP. (Since you do not have this move in Gen 1, attempt to get its HP in the Red Zone by using non effective moves when in the orange zone. It should not be too difficult)

A Pokémon that can inflict a Freeze or Sleep will be nice, since it boosts the catch rate by a fair amount (Twice the amount of Paralysis, Poison, and Burn) http://www.gamefaqs.com/ds/960100-pokemon-soulsilver-version/answers/179569-status-effect-and-how-they-affect-catch-rates

The Pokéballs I would recommend are Quick Balls (Start with these in the Early Battle), Ultra Balls (Good for any scenario, if you don't want to use special Pokéballs, stick with these), and Timer Balls (Since the battle typically takes a while, so use this later in battle). You may also want to use a dusk ball since it is in a cave. Edit: I found out you are in Gen I, so Ultra Balls are your best bet.

Bring a Pokémon with Taunt or Heal Block since Mewtwo will recover itself very frequently. Make sure this Pokémon is bulky so it may last longer.

EXTREMELY IMPORTANT. DO NOT FORGET TO SAVE BEFORE FIGHTING THE POKÉMON. Good luck to you.

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False swipe didn't exist in generation one (http://pokemondb.net/move/false-swipe). And yeah, the best ball in Generation 1, besides the master ball, was the ultra ball. Everything else looks good though.
Thank you for notifying me!