Where do you get gems from?

Answer 1

i think you have to beat the elite four to get it, afterwards take it to celio for a rainbow pass, which unlocks islands 4-8

Nope, wrong. Beat the Elite 4 once. You should've caught at least 60 different Pokemon after that. Once done talk to Prof. Oak and Gary will come. Prof. Oak will give you the National Dex. Go to One Island, talk to Celio, and go up the mountain. Find 2 team Rocket members and beat them. Go inside the cave they dug, and look for the ruby gem. Go back to Celio and he'll give you the Rainbow Pass to Islands 4-7. The sapphire gem I don't know. I'll tell you how to get that gem when I find out. Good luck.

Answer 2

Originally you find it in the cave called dotted hole but when you get the sapphire it gets stolen from you you end up going to the rocket warehouse and defeating the robber to get it back.