Well, you either catch it, or use a Pokemon that knows thief without having it holding an item.
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i do believe you can steal them from paras and parasect. its rare that you'll get a big mushroom though (you mostly get small mushrooms)the best way to do this though is to get some parasects and parases in the safari zone. it is about 90% of chance of them having either two tiny mushrooms or a big mushroom. the reason I say 90% is because I never caught a paras or parasect without them have a mushroom or twoparas and parasect will sometimes be holding mushrooms ( big and little).Paris sometimes have mushrooms as an item in the wild. either catch them and hope they have small mushrooms or use the move thief to steal them, if they have them that is. Paris are everywhere but there are alot of weak ones in mount moon
go to the moon cave first then go down some stairs where all the wild Pokemon are paras teach a Pokemon thief so you can steal there mushrooms you are more likely to get a tiny mushroom rather than big mushroom if you use thief and you get nothing don't bother agagain because that Pokemon isn't carrying anything oh and thief still works if you make the Pokemon faint :]
The move tutor lives in Two Island, you need to bring two tiny mushrooms or one big mushroom and your Pokemon needs to be able to learn False Swipe. The only ones I know from the top of my head are Marowak (lvl 39) and Scyther (lvl 16). To be able to find the mushrooms, go to Mount Moon and catch Paras, they are often holding them. Or teach the move Thief that you found in Mount Moon to one of your Pokemon and have them use the move on the Paras to steal their mushrooms.
The Second Gem is in the Dotted Hole in 6 island, although when you get there a scientist will steal it and you have to got to the rockets base on 5 island and then you have the Second gem
You have to A: Be them or B: hack their account