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In Alpha sapphire, I'm chaining on Route 101 for a shiny Zorua.

I find one, but the NPC walks over the patch and the Pokemon disappears, giving me the message that it ran away.

Does this kill my chain?

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According to Bulbapedia:

A chain is broken when the player leaves the area (including entering a building), encounters a wild Pokémon that isn't hidden, or moves too quickly and scares away a hidden Pokémon.

Hidden Pokémon can be encountered for a chain either with or without the Search function. Getting the message "The Pokémon couldn't be found. Try looking in a different area!" when using the Search function does not break the chain.

So I'm pretty sure that if someone scares the pokemon it will break your chain.

  • but does the npc stepping on the hidden pokemon's patch and giving me the message "it ran away" break my chain? – 8bitm Jan 15 '15 at 23:10
  • Yes, scaring the Pokemon will break your chain, it doesn't matter who scares it. The only message allowed is "The Pokémon couldn't be found. Try looking in a different area" – pinckerman Jan 15 '15 at 23:11
  • The same source also states that "If an NPC attempts to move through a hidden Pokémon, they will be stuck against it until the Pokémon moves." This means that NPCs shouldn't be able to scare them away and the Pokemon was probably accidentally scared away by OP at the same time as the NPC tried to move into that spot. – scenia Jan 23 '15 at 9:54

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