How to Get Mewtwo

Go to the Secret Lab in Port Decca (same place you find Mew) and a cutscene will begin with Mewtwo and then he becomes a roaming pokemon! (Can find anywhere in the wild)

You need to have done the Mew encounter first before you can see the Mewtwo cutscene (Once you unlock mew in the wild you can leave the building and re-enter for the Mewtwo cutscene to begin.)
Here is a video that helps!