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Probably the biggest site for NIMH fanfiction, it hasn't been updated in over a year, but it still has many exceptional stories.
Evondral: It's been a little over 2 years now, there site still has it's fiction and art up, but mysteriously it has not seen any updates at all. The webmaster Simon is aware of this and is calling for anyone with fanfiction to submit.
The site has seen a recent series of updates in the forms of a continuing story by David Leemhuis - Mrs Brisby and the Search for Johnathan - and a reboot of NIMH: The Final Experiment in purely written format. YMMV.
As the title implies, a fan site for the two biggest pieces of girls' fanservice ever to be rats. In addition to fanart, contains the good fanfic Freeze Frame, listed below, and links to other handy sites.
Essentially the center of the NIMH fandom at this point, the Muck is mostly active and some RP still goes on. New members are always being accepted. The Muck itself started from a masterfully written fanfic, "The Rats of Thorn Valley", which can be found below.
Stories focused on the family and the friendly relationships of the cast. Plot-focused stories or light day-in-the-life stories. Pretty much anything that isn't focused on romance.The Secret of the Stone by Procyon
Synopsis: It has been roughly 2 and a half years since the events of NIMH. Life moves on for the Rats and the Brisby family, and all live peacefully in Thorn Valley. But when NIMH returns at the old farm home, what ill omens do they carry? And just what mystery does Ms. Brisby and her family hold?
Comments: Well written, compelling, and surprisingly in-character. The story really smooths into the continuity, and there's definitely something for everyone here. It also comes with some great illustrations. Sadly, the author leads a very busy life, and as such the Fic as been on hiatus since 2004. It's not known if he will ever pick it back up again, but there's always the chance.
Synopsis: (Taken right from the site) Four months after the events of the movie, Mrs. Brisby and her children eagerly accept an opportunity to visit Thorn Valley; but unknown to them, the Rats of NIMH are once again facing a deadly peril—one which could destroy their self-sufficient paradise forever.
Comments: Probably the best NIMH fanfic ever written, so good that it inspired the creation of NIMH Muck. The fic itself is astoundingly well-written, keeping everyone in character and painting a clear, vivid picture of life in Thorn Valley, all the while wrapping us up in a grand plot. Sadly, Paul S. Gibbs died in 2002, but not before finishing both this and a sequel double the size. Read it, enjoy it, and see how it's done. The Sequel can be found below in Shipping Fics.
The NIMH Network by Steve Vanden-Eykel, who runs the excellent N.I.M.H. Archive (where this fic is hosted)
Synopsis: From the author: "Nimh was a great movie, but it did leave several unanswered questions, the biggest of which was the Stone. I mean, let's face it, the Stone sticks out of that plot like a sore thumb. After seeing the movie, I started to think about these questions, and after a while, a story started to take shape. I began to see Nimh as the middle act in a three part story."
Comments: A two-part fanfiction that addresses (funnily enough) some of the issues brought up in Wild Mass Guessing and It Just Bugs Me, though it is quite old. Turns the film into the middle of a Big Damn Epic and (as usual) comes up with a smarter sequel than the official one.
Pairings: (Nostalgic) Mrs. Brisby x Jonathan Brisby; implied Mrs. Brisby x Jacob (OC)
Synopsis: After a dream, Mrs. Brisby is disheartened to find that she's remembering less and less about Jonathan. Daughters Teresa and Cynthia and to some extent son Martin attempt to cheer her up, but are interrupted when Timothy comes in with big news: another survivor from NIMH has been found. Mrs. Brisby is intrigued by him, but he has big news.
Comments: Another unauthorized sequel, this one equally excellent, and in high quality graphic novel form. Now that's dedication. Sadly, it appears to be permanently incomplete. Sound effects are in Japanese, but the text is translated into English.
Pairings: Justin x Judith (OC), Elizabeth (Mrs. Brisby) x Jonathan (Canon)
Synopsis: (Taken right from the site) The Rats of NIMH and the Brisby family anxiously prepare for their first winter in Thorn Valley. Meanwhile Jonathan learns the meaning of "long-suffering" as he battles trouble with work, family, weather—and, most perilous of all, the fallout from Justin's tortured love-life.
Paul S. Gibbs's follow-up fic to The Rats of Thorn Valley. Just as well written and even longer than his first work, Second In Command is something any NIMH fan should read when they've finished Rats of Thorn Valley.
Note: I posted it here because the fic carries a strong romantic overtone in comparison with the first.