This riddle isn't PokemonHero's, it's my own. I wasn't guessing Absol for it. Spiritomb has already been guessed, and is incorrect.
In confused lands I am found,
Near the top, or underground.
Frost, mist, and darkness are where I stay,
Even though I summon a storm or ray.
Reach into your item case,
And I can alter time and space.
Incorrect: Smeargle, Arceus, Giratina, Dialga, Palkia, Ditto, Mew, Darkrai, Kyogre, Misdreavus, Spiritomb, Castform, Rayquaza, Celebi, Rotom, Frosslass.
Hints: It is not a legendary Pokemon. It does not evolve using an item.