OK you need to do this.
1st- Go to 1 Island Mt Ember, beat the Rockets (they give you a password) and go in, and find the Ruby.
Take it back to Celio and he gives you the pass for Islands 4,5,6, and 7. Now go to 6 Island Dotted Hole and cut down the door.
Go in solve it, and take the Sapphire. A scientist will take it and leave a password. Go to 5 Island Rocket Warehouse and beat him. Take the Sapphire back to Celio.
Now you can fight Mewtwo.