This is wholesome and I’m viewing it as canon.
But I’m also laughing at the thought of those magical Poké-tears launching into goddamn space and reconstructing Mewtwo from atoms.
For me, Mewtwo would be revived by the tears of the pokemon they protected, including even Shadows (Just like Pokemon the first movie)
After healing Shadows wounds, they'd ask him to keep G.U.N away from the forest. Shadow is still welcomed and both occasionally train together.