PokéBase - Pokémon Q&A
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No sites make this clear. Does anyone know?

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After battling against Blue for the first time, the Pikachu will choose to stay out of its Poké Ball and follow the player around unless he faints, is put into storage, or is traded.

Hope I helped. :)

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Another thing to note is that if you DO decide to put Pikachu in the box in Yellow, it's Happiness decreases. Just some food for thought.