Assuming Lore/Manga/Anime feat scaling rather than game stats (since Zapmolcuno doesn't have game stats to quantify it's ranking), Mewtwo stomps in it's base form alone due to being around base Deoxys' level who can compete with a Multi-Continent level mon like Rayquaza. If going with in-game logic and treating Zapmolcuno as a Mega-esque boost, then it likely wins purely due to Psystrike on a special attacker being a hindrance and Mewtwo not having anything substantial to use on Zapmolcuno, who can just heal itself with Roost.
Magical Journey Mew (Amnesia, Psychic, Aura Sphere, Ice Beam) runs the Cell Arc Gauntlet
- This manga spinoff version of Mew was capable of creating a dimension the size of a Large Star and is Sub-Relativistic in speed.
- Mew has Mewnium Z to use Genesis Supernova, but can only be used against one opponent.
- Gets HP and PP fully restored after each fight.