Lin is the second last boss, then El sends out his Ditto, it copies you, and it has a team of pokemon that are identical to yours except they are all 3 levels higher (or level 100).
Edit: Or just a team of the 6 best legendaries in the game coming to test your worth.
Ex) Mewtwo, Lugia/Ho-oh, Rayaquaza, Arceus, Best Gen 5 pokemon, Best Gen 6 pokemon
(I really only know the first 3 gens...)