Known as ‘Project M’, the Mewtwo side mission in Pokemon Legends: Z-A gives you the chance to add the Genetic Pokemon and both Mega Mewtwo X and Y to your team, but you need to unlock the side content by acquiring a certain Mystery Gift first. Even then, you can’t access this particular quest right away.
There is not only an unlock requirement to access the mission, but you also need to visit a key location in Lumiose City. This detailed walkthrough will take you through how to start the Mewtwo mission in Pokemon Legends: Z-A, how to complete it, what the Legendary’s weakness is in order to beat it easily, and which of its two Mega Evolutions is best.
How To Start The Mewtwo Side Mission
In Pokemon Legends: Z-A, the Mewtwo side mission can only be accessed if you’ve beaten the game’s main story and have the Mewtwonite X and Mewtwonite Y Mega Stones with you in your satchel, as you visit its starting location of Floor B3F of Lysandre Labs.
This lab is under Lysandre Cafe, which you would have visited during one of its many missions in the story: specifically, during Main ‘Mission 35: Reaching Rank A’ , when you find out more about the ultimate weapon. Since then, nothing else would happen if you enter the lab, but the Mewtwo side mission will start once you have the Mewtwonite Mega Stones with you.
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How To Get Mewtwonite X and Mewtwonite Y Mega Stones
You and other Pokemon Legends: Z-A players can get both the Mewtwonite X and Mewtwonite Y Mega Stones as a bundled Mystery Gift from the Link Play menu, which is also used for battling other Trainers in Ranked Battles. In the game, press X to open the menu, select ‘Link Play’, ‘Mystery Gift’, ‘Get via Internet’, and ‘Project M’ once you’re connected to the internet.
While an internet connection is required, you do not need a Nintendo Switch Online membership to access Mystery Gifts.
After the typical animation of a present opening, as is normally the case with Mystery Gifts in Nintendo Switch Pokemon games, Mewtwonite X & Mewtwonite Y are yours — instantly added to your Legends: Z-A inventory, along with the Mewtwo side mission, ‘Project M’, becoming available.
As soon as you walk into the lab section of Floor B3F, your new Mega Stones will be detected, Project M will activate, and Mewtwo will be released if you choose to ‘release the locks’. With a quick unlocking sequence, Mewtwo shall appear in front of you, and Mable will suddenly chime in over the Pokédex phone.
After warning you how ‘extremely dangerous’ the Legendary Pokemon is, and that you, of course, ‘better not fail to catch it’, Pokemon Legends: Z-A’s ‘Side Mission EX2: Project M’ will officially start at last. You’ll then regain control of your protagonist and get the chance to prepare for the battle.
How To Beat And Catch Mewtwo
Mewtwo’s Weaknesses
Just like in other games in the franchise, Mewtwo in this Pokemon Legends: Z-A side mission is a Level 70 pure Psychic type; that means it has not just one weakness, but two: Dark- and Ghost-type attacks, which can wear Mewtwo down and defeat it easily before trying to catch it.
At such a high level, you will need a team with at least four or five Pokemon Level 70 and above to withstand its attacks. For instance, Feraligator learns the Dark-type Crunch naturally, or Alakazam can learn Shadow Ball via TM 74.
Although you would have needed Pokemon that strong to defeat Legends: ZA’s final bosses in the campaign and make it this far anyway, so that likely shouldn’t be a trouble for you.
Best Poke Balls For Mewtwo
Being able to actually defeat Mewtwo isn’t really the issue with its side mission in Pokemon Legends: Z-A; it’s rather its very low catch rate. If you wait until you’ve depleted its HP before getting ready to toss your chosen Poke Ball, as you would for any other Pocket Monsters in the game, it has a very high probability of breaking free and ending the battle.
Defeating Mewtwo by making it faint in Legends: Z-A doesn’t mean you’ll miss your chance to catch it. In fact, Mable will yell at you for being too strong, and the side mission will reset to before you approach Mewtwo for battle to try again. However, if you fail to catch the Psychic Legendary numerous times, those extra seconds walking back over and restarting the battle sequence certainly add up and become a nuisance.
To make catching Mewtwo much easier in Pokemon Legends: Z-A, spread out your catch attempts by getting it down to just a sliver of health first, then throw Timer Balls or Ultra Balls until you’ve either caught it or it becomes agitated (when Poke Balls no longer work until you defeat it fully).
Besides the Master Ball, Timer Balls are the best for catching Mewtwo in this Legends: Z-A mission, since their effectiveness increases the more the target Pokemon attacks. If your team is bulky enough, it should be able to withstand the ten or 12 attacks that are necessary to start using Timer Balls effectively.
You still might have a lot of trial and error with said catch rate being so low, but outside of getting the Master Ball as your last Mabel’s Research reward, Timer Balls are your best bet for catching Mewtwo during the five ball throws you’ll have before accidentally defeating it and having the battle reset.
Use Status Effects
To pair with Timer Balls, you should also use moves that inflict status conditions; Burn, Confusion, Drowsy, Frozen, Paralyzed, or Poison; for a better chance of catching Mewtwo in this Legends: Z-A side mission, since it increases Pokemon catch rates ever so slightly.
The difference may only be minimal, but it can be enough to make it a successful Poke Ball throw. In our case, it took us five battle attempts to finally catch Mewtwo in Z-A, but it wasn’t until our Clefable paralyzed Mewtwo with a Thunderbolt that the Timer Ball actually worked.
With Mewtwo finally caught, the game will cut to Mable talking for a bit about how Team Flare originally caught Mew’s clone in the Kalos region’s Unknown Dungeon from Pokemon X and Y — to hopefully use for the ultimate weapon. She further explains how, after a failed attempt to utilize pieces of the Mewtwonite X & Y for Mega Evolution, Mewtwo and its Project M was essentially shelved and forgotten about until now.
As the Project M side mission wraps up, you’ll be rewarded with 10,000 Poke Dollars and an Exp Candy XL for your efforts, and now, you’re able to freely use Mewtwo (and its Mega X & Y evolutions) in Pokemon Legends: Z-A.
Is Mega Mewtwo Y Or X Better To Use?
If you’re looking for the best version of the Legendary Pokemon to use in Legends: Z-A, Mega Mewtwo Y is objectively the better choice over Mega Mewtwo X, due to its better move pool to make use of its massive Sp Atk stat and Speed. As its base form is also strongest in Sp Atk, it’s far more consistent to utilize Mewtwo as a special attacker as a whole — compared to it being a relatively weaker if having to rely on physical moves as part of its moveset for Mega Mewtwo X, which would partly be a hindrance when not Mega Evolved.
However, while Mega Mewtwo Y was a far superior choice compared to Mega Mewtwo X in past Pokemon games, that margin has narrowed significantly in Legends: Z-A — to the point where making your Mewtwo hold the Mewtwonite X instead would actually be the right choice depending on the situation.
The key differences between Mega Mewtwo Y and X are their typing, ideal movesets, and stats: Y has stats more suited to Special Attack with decent Speed and still being a pure Psychic-type, while X has a higher Attack stat with bulkier defensive stats, along with also being a dual Psychic-Fighting-type.
In the traditional turn-based system of Pokemon, Mega Mewtwo X’s slower Speed, lesser movepool, and added Fighting-type would be to its detriment. It would not only be weak to Flying and Fairy-type attacks, as well as Ghost, but its slower Speed would also mean it could get wiped out before it could strike back.
By comparison, Mega Mewtwo Y’s larger movepools could mean it has far more coverage — plus being quick and strong enough to sweep enemy teams easily. In Pokemon Legends: Z-A, with its real-time battle system, Mega Mewtwo Y can still be a sweeper, but its weaker defensive stats make it much more of a glass cannon.
Mega Mewtwo X, on the other hand, can make use of Legends: Z-A’s battle system and its added bulk for more survivability, as it will be more likely to take a hit or two before attacking back.
What’s more, if you combo its moveset with Amnesia (boosts Sp Defense), and Bulk Up (boosts Attack and Defense), you’ve got a nice, long-lasting all-rounder that could quickly dominate the Battle Royale or the latest multiplayer season with the right type match-up.
Altogether, Mega Mewtwo Y is still the best Mewtwo Mega Evolution to use in Pokemon Legends: Z-A — since it has so many more usable moves for type coverage with such strong Sp Atk, and its defenses. That’s also because Mega Mewtwo Y can be effectively bulked up as well with Amnesia and Reflect.
Nevertheless, if you want to EV- and IV-train your Mewtwo to be more of a physical attacker with the Mewtonite X, to better fit in with your specific team, no one at all should blame you.
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