PokéBase - Pokémon Q&A
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According to the website, some Pokemon have hidden abilities, such as greninja having the hidden ability protean, but then when I use greninja it doesn't do that and then when I did an online battle the opposing greninja could do it, so i'm confused... how does it work?

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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!

Source: Experience

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Tyrantrum does have a Hidden Ability, Rock Head, it just isn't obtainable yet.
Could have sworn I edited that to Aegislash
It's probably good to note that in Gen 8, one can use an Ability Patch to turn a normal ability into a Hidden Ability. I've never attempted this myself, but it can be done.
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Each species of Pokemon has one or two "standard" Ability slots, and one Hidden Ability (HA) slot. When you encounter a Pokemon, the game randomly chooses which Ability slot it has. HAs are special, because in most circumstances, the game will never allocate the HA slot.

Individual Pokemon can only have one Ability at a time, depending on which slot they have. Your Greninja doesn't have Protean, simply because it wasn't given the HA slot. Instead, it has the standard slot Ability Torrent.

The starter Froakie you get at the beginning of the game will always have a standard slot, which means it will always have Torrent. To get a Protean Greninja in Gen 6, you must capture a Frogadier from the Water-type Friend Safari or trade for it.

For more information on HAs and how they work, see this article on Bulbapedia. For more info on how to get Pokemon with the HA slot, see this question. Note that HAs only exist as of Gen 5.

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Ok. Thanks for that, I was kind of wondering what that person said on how "pokemon in hordes can have rare abilities". Also I just got a water friend safari, so now I something to look forward to doing.
No problem :D
btw you aren't guaranteed to get a Frogadier in your Safari. If you are lucky though, you'll be able to evolve a Hidden Ability Frogadier.