How To Get The Ruby And Sapphire:

Ruby:
After you beat the elite four the first time and have 60 pokemon talk to Proffesor Oak he will give you a national dex (this allows you to see and capture johto,hoen pokemon)
After go to island 1 and talk to celio he is the scientist right in the pokemon center he will say thet he needs a Ruby plate and a sapphire plate. So surf north to Mount Ember(If you didnt catch Moltres catch him now it is on top of Mt.ember)go right there will be two rockets talk to them and you will be in a battle defeat them and they will tell you a password then go in the cave eventualy you'le be in this foggy place there will be a red plate and talk to it and you got the ruby. After give it to Celio and he will give you rainbow pass now go to island 4.
Head east then surf north and head in the cave. First go in the hole and somehow get HM.7 then teach it to a pokemon after go up the waterfall and go down the stairs Lorilie will be there then she will tell you to beat the rocket beat him and go to island 6. Head down and you will see a cave anyways use cut and the door will open. Go in and go down than go Down the hole north then south then west after east talk to the sapphire and then a scientist will snatch it away he will tell you the last password then go to island 5 and go down to rocket hideout Do anything you can to get to the scientist he is on the top.
After when you beat him he will give you the sapphire give it to Celio and you can get hoen pokemon. Now you can go to Unknown Doungeon and you can face the elite four again.
Warning: they are 12 lvs higher!