You can get it after you beat the elite 4,got the national dex,and got the ruby and saphire plates to Bill
This red/blue colored guy thats guarding the cerulean cave will then move out of the way so you can get in,theres strong pokemon 48 and up,use mac repel and search for an icon of Mewtwo,when you find it,it will be in a dead end of water,save before you battle it