Yes, but also no. Nintendo sued the creators of the free Pokemon Uranium fan game, and the original creators were forced to step down and leave the project. The only reason it still exists is because the new team remains anonymous so they can't be sued.
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This is false.
Pokemon Uranium devs took the download links down of their own accord - they hadn't received even a Cease & Desist at this point, let alone a lawsuit. TBF - it may have been correlated to Pokemon sending C&E to a few third-party sites that were hosting Uranium alongside pirated content with less-than child-friendly advertisers. Nintendo's attitude on piracy is well-known, but they actually barely pursue legal action against piracy platforms (beyond telling them to take links down) these days either.
Let me know if you have any more questions.