First, you must defeat all the gyms, dojos and champions.
Afterwards, you can find Kyogre, Arceus (Water), Lugia, Articuno, Yveltal, Genesect, Regice in Map 9.
For the fire legendaries, just search in Map 10.
For Dialga, Regice, Articuno, or anything else that is Ice Type, go to Map 11.
For Deoxys, Rayquaza, Mew go to Map 1.
For Electric Legendaries, go to Map 12.
For Latios and Latias, Map 6?
Go in Map 27 near the stairs, you can find a Mespirit.