The elite four will be in the Pokemon league.
the elite 4 should be on route 22 where the indigo plateau is
beat the elite 4
get a job life.
beat the elite 4 and then get sapphire stone
you have to start with squirtle and beat the elite 4
if u battled him in the gym do the elite 4
After you beat the elite 4 in will roam the region
beat the elite 4 alot
explore around and catch mewtwo.
well just go to the place that the elite 4 is at and do what you did the first time
but before this, you must have defeated the elite 4
you have to beat the elite four and have a national dex