You befriend the three Legendary Birds-Articuno, Zapdos and the fire one- go to their
island in the friend areas and then you can go to another area where there's another
legendary.

First go to mount faraway recruit Ho-oh then the other birds. Wen you have them all there
will be a cut scene with them saying something about the silver trench. You go there
through all 99 floors, Beat Lugia, Recruit him, And then somewhere later theres Deoxys