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Does Nintendo actually have a hand in Pokemon Go? I don't know what the relationship between Nintendo and the Pokemon Company is.

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They own a piece of The Pokemon Company and a piece of one of the companies that owns a piece of The Pokemon Company. No one really seems to know if that amounts to a controlling interest or not.

But empirically, it seems unlikely an independent Pokemon Company wouldn't put out Pokemon games for non-Nintendo platforms.

Well, Pokemon Go is a non-Nintendo platform, so it could go either way (maybe Nintendo did it to increase the value of the franchise, maybe the Pokemon Company didn't do it more to avoid diluting it).

The announcement of Mario Run seems like a pretty clear indication that Nintendo has shifted, some time in the past, to thinking of phones as not competing with their consoles/handhelds. Pokemon Go and Mario Run may have begun development concurrently for all we know at this point.

They (along with Google and the Pokemon Company) also invested up to $30 million into Niantic, the developer of Pokemon Go a year ago [1].

[1] http://www.recode.net/2015/10/15/11619616/nintendo-google-to...

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