You have to get the Eon Ticket from Norman after beating the Elite 4:
In Pokémon Ruby, Sapphire, and Emerald, the player must first receive the Eon Ticket from Norman. With the Eon Ticket in the Bag, the player must then attempt to board the S.S. Tidal from the Lilycove City Harbor. A Sailor will replace the usual guide, taking the player to Southern Island. In the center of the island's forest there is a mysterious sphere; upon interacting with it, the player will be attacked by a wild Latias or Latios (whichever did not roam Hoenn).