Sadly, if you create fan fiction, you're very quickly in the realm of copyright infrincement. It's very hard to do serious fanfiction without committing some form of copyright infringement somehow. It is so bad that sometimes, courts interpret copyright so broadly that they even consider mere characters as copyrightable. Which means you might not even be safe even if you did not copy anything verbatim. The only way to be 100% safe is to distort your work so much that basically only allusions to the “original” remain, but that's obviously completely besides the point of fan-fiction. That's the thing! Fan fiction is only fan fiction because you
want to stay “true” to the source material.
Long story short, fan-fiction is basically impossible to do legally. Copyright sucks.

This is one of the examples that shows
how much power people are granted with the excuse of copyright. The power to strike down the creative work of others … Ironic, considering that copyright allegedly is there to incentivize creative work.

Anyway …
The ONLY reason why most fan fiction is not attacked is because the copyright holders usually tolerate them for various reasons. But there is no legal reason that I know of that prevents the copyright holders of the source material to strike down fan-fiction. I think the main reasons why they (usually) don't do that is: 1) Fear of reputation loss (you'd basically attacking fans and risk a shitstorm) and 2) They don't perceive it as threat. But that's only a guess.
This makes me wonder: Is there some kind of “exit strategy” when Day X arrives and Nintendo goes into full attack mode? I mean, the games are still games in their own right and absolutely deserve to exist IMHO. It's not like they are just rip-offs, there's still a significant own creative work involved in these games, that's something that needs to be stressed.
Even if you are forced to take things down, these games should at least be securely archived/backed up somewhere, for the future, if copyright ever is changed to the better (or even abolished).
I would also organize a massive shitstorm and make yourselves heard when Day X arrives. It should be made clear to the corporate world that attacks on fan-fiction are NOT possible without consequences.
