Ruby and Sapphire Wallkthrough.
Ruby gem is on Island 1. On Mt. Ember Cave. Two rockets are blocking the entrance and they will only leave if you beat them and you probably will be able to beat them.
Sapphire Gem: Ok.. this one gem make's the game but more complicated and bit drastic. After you got the rainbow pass go to island 4. You must bring a useless water type pokemon so you could teach it the move Waterfall. Yes it is there you will find the HM Waterfall. After getting the HM..go up to the waterfall and you will find the Elite 4 member Lorelie trapped by Team Rocket Grunts' Help her beat them and then she will ask you to save the other pokemon. Now you must go to Island 6. Now bring a pokemon that knows the move Cut. Now go in front of the door. Use the move cut and it will open. Enter the cave and go to the middle hole. You will end up on a dungeon with four different holes. Here’s what you need to do. Go to the Top hole, then left, right and bottom and you will ended on a cave go to the hole and you will find the Sapphire gem but a scientist will take it from you and you MUST get it back. Now go to Island 5 and go to the Team Rocket's Warehouse. Beat all of them including the Scientist and after that he will give back the Sapphire Gem. Now take it back to Celio and the machine will be fixed and you can now trade to Ruby/Sapphire/Emerald/XD and Coliseum.
If you are trying to go back and try to challenge the Elite 4 again. You must be aware that they have been stronger than ever. Their pokemon's level change as well as they gain new pokemon