Question

I have a pokemon with protect and wondergaurd will it still hit even if I use protect or detect?

Answer 1

Protect will cover it.

Answer 2

No, protect/detect blocks everything except feint, which does not affect shedinja anyway

Comments

Actually the moves thunder and blizzard can break through it 25% of the time if it is rainy or hailing respectively.-granted neither of those affect shedinja.

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And don't forget about Shadow Force

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@DarkTyphlosion: if it is hailing then Shedinja will get hit by the hail and faint.

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I'm only talking about direct attacks that will hit him in that turn, not passive damage that affects after the fact.