Nintendo has been cracking down hard on unauthorized fan games using their IP in recent months, shutting down projects like AM2R: Return of Samus and No Mario's Sky. The most well-known recent case of Nintendo vs. unlicensed fan projects is probably Pokémon Uranium Version, a fan game almost a decade in the making.
Uranium racked up 1.5 million downloads in days after launch, but download links were quickly removed due to the possibility of legal action from Nintendo, and all development on the game officially ceased shortly after. According to the game's creator (who goes by Involuntary Twitch), this is because Nintendo threatened to sue him for "hundreds of thousands of dollars."
"In retrospect, there was absolutely no way this could continue indefinitely. The final nail in the coffin was on September 1, when I received a letter at my front doorstep from the legal firm that represents Nintendo of America. It was printed on nice quality paper, and had been sent via express overnight shipping, so that's how I knew it was serious. It told me that I needed to immediately stop our entire web operation – take down the server, stop providing updates and stop generating ad revenue – or they'd sue me, and the Uranium Team, for hundreds of thousands of dollars in damages." — Involuntary Twitch
Nintendo has yet to comment on this claim, so we're only hearing one side of the story. Nintendo has been increasingly more aggressive in protecting their IP lately (they even put out a hiring ad to expand their ability to do so last month), so there's little doubt that they'd want to shut a fan game like Uranium down, but we've yet to see proof of specific dollar-based threats from the company at this time.
Source: Involuntary Twitch