Getting the Sapphire is a bit tougher.(you might want to by some max repels) Once you get to Six Island, go to the Ruin Valley south of town. In the center of the valley is a place called the Dotted Hole. To get inside, go to ise fall cave in Pokemon fire red/leaf green and use waterfall the go up the ladder, and go into the dark cave in front of the ladder then you will se Lorelei of the elite four surrounded by team rocket members; talk to her then start trying to leave them, she will ask you to help her defeat the rockets. After you defeat them talk to her again, then leave ice fall cave, go to the dotted hole and the scientist wont be there, use cut on the door and your in.
Once you get to the back of the cave, you'll find the Sapphire, but before you can take it, a Rocket Scientist will come and take it to the Rocket Warehouse on Five Island. Go to the Warehouse and find the scientist. Defeat him and get the Sapphire from him. Take the gems back to Celio on One Island and he will upgrade his machine. You can now trade with the games Pokemon Ruby and Sapphire!
You have to go to the seven islands and go to island 5 and team rocket should have it in there building, or you go to island one and go to the volcano where moltress was and team rocket will break a hole in it and you find it in the whole.
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for the ruby gem go to mt ember.....as you get in you will see tow rocket team members in the front of a cave.fight with them and they will go.in this cave is ruby gem.the second(sapphire gem)is in 6th island in the cave.(for ruby gem..caught moltres get away and after they will fight with you...i hope i help...