In order to have something, you must get it from some source or something. You can't just have. That just is a giant slap in the face to logic, and only video games can do that.
What I mean here is that you first must catch a Pokemon with a hidden ability to have its hidden ability.
Hidden Ability Pokemon can be caught from Horde Battles and the Friend Safari in X & Y (not guaranteed, but there is a chance), and the Dream World (R.I.P. :( ) and Nature Preserve/Hidden Grottoes in Generation 5.
What is a hidden ability?
A hidden ability is a potential third ability a Pokemon can obtain by certain means only in Generation 5 and above. This means some Pokemon have Hidden Abilities, and some do not. Some hidden abilities can also not even be obtained, but are in the coding. For example:
Serperior: Contrary - Not Available
Camerupt: Anger Point - Available thru Friend Safari
Aegislash: ??? - Doesn't have a Hidden Ability
How do I get a hidden ability?
As stated before, you must have the Hidden Ability when the Pokemon is captured. Otherwise, that Pokemon doesn't have its hidden ability.
Say you want a Effect Spore Vileplume. Kewl! First, you must capture a Oddish/Gloom from the Friend Safari with its hidden ability (Run Away or Stench respectively). For Gloom's stench, you can keep using physical attacks on it. If you flinch, it has Stench. You can then evolve that into a Effect Spore Vileplume.
Same with that Greninja you're itching for. Catch a Frogadier in the Friend Safari. See if its attacks change type when it attacks. If they do, then catch yourself the Protean Frogadier and evolve it into that Greninja!