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So Team Flare decided to set their plan into motion:

Activate the ultimate weapon to wipe out all who aren't part of Team Flare.

Naturally, I went to stop them, but now I have to choose between pressing a red button or a blue one.

The scientist I just defeated told me that one of the buttons will activate the device, while the other will shut it down, but he didn't tell me which.

Knowing the Pokémon series, I doubt I can make a wrong decision, but I still get the feeling that choosing one button or the other may result in subtle-to-moderate differences in the game later on, such as which Legendary I will meet where, or similar.

What will happen if I decided to press the red button? What will happen if I choose the blue button? Or does it really not matter at all?

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    Man, we've come a long way from Team Rocket trying to steal a Pikachu... – tombull89 Oct 17 '13 at 11:15
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    Hasn't anyone ever told you not to push the red button! – C-dizzle Oct 18 '13 at 18:27
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    @C-dizzle Not really. I was taught to "Push every button you encounter, and if it doesn't solve your problem, push the buttons some more". Eventually, I decided to solve my dilemma Matrix-style and took the red pill- I mean, the red button :p – Nolonar Oct 18 '13 at 18:31
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Either way, the ultimate outcome is the same, as

The machine was going to be activated anyway, whether by you or them. He himself says he would have activated it anyway had you pressed either button.

There doesn't appear to be any difference in the later game based on your choice.

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Red button - activates it Blue button - Deactivates but scientist still activates it

Bummer indeed, but yeah either way the thing still gets activated and you will still have to chase to stop it.

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The Blue button shuts it down and the Red one activates it, but either way it gets activated, you'll see.

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If you press the red one you activate it, but if you press the blue one xenoric activates it via remote control.

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