You completed the main story before encountering Mewtwo. Necroflame encountered it after assignment 5 and got it as a mid game legendary as intended. Young Mewtwo is the default encounter and the lore explanation for you encountering normal Mewtwo was that during the course of the story it matured.
You can take young Mewtwo to a hidden room in the cerebral complex to make it mature.
You can take young Mewtwo to a hidden room in the cerebral complex to make it mature.