In story mode, you will have to fight Zapdos, Moltres, and Articuno.When u beat them they wont join your team because 1. you didnt beat the game yet, and 2. you might not be a high rank.After the credit roll, u can go back and fight them again,but they still wont join your team, because you dont have Legendary Island. To unlock Legendary Island, you have to do a rescue mission that was sent to you by mail,check the mail and see the reward, it will say friend area(not all the time).You cant by Legendary Island.So when u get Legendary Island, you can go back and fight them again and they will join they team.