The one that started it all. For those that haven’t read it, HPMOR is an alternate world story where Petunia married an Oxford Professor and Harry was raised with an understanding of science and rationality.
I would humbly suggest beginning here, where I rewrote the first four chapters, and then picking up at chapter 5 at the website. The original early chapters were a bit bare in terms of characterization and setting, and I wanted to try and hint at some of the depth and genius of the later story earlier on.
Twilight fanfiction where Bella isn’t just not-useless as a character, but is a rationalist with a mostly sane perspective on finding out that mega-powerful-no-downside vampires exist. Has a sequel and lots of spin-offs stories that are also worth checking out, though your mileage may vary on each.
Golden Age Superman rationalfic where Lex Luthor is the protagonist reacting to the idea of an alien god descending on humanity to dispense uncontestable justice. Kind of ruined Batman vs Superman for me before it even came out, since I knew it couldn’t possibly cover the themes as well, however hard it tried.
Terminator rationalfic where Sara Conner is a computer scientist and programmer who actually understands the implications of time travel and how to take advantage of it. Similarly ruined Terminator: Genisys and all other potential Terminator movies, though those have been crap since 2 anyway.
Back when I was considering trying my hand at a rational story there were a few ideas I had about what to do it on. Animorphs was near the top of my list, and I enjoyed participating in all the brainstorming in /r/rational both because of my love for the source material and how it teemed with such great possibilities.
Eventually I decided to go with Pokemon, and I’m glad I did for a number of reasons, one of which is that whatever Animorphs story I wrote would have been a feeble shadow of The Reckoning. This story is everything I ever wanted in a rational animorphs story, and more importantly, what I didn’t even know I wanted. If you’re a fan of the canon work at all, you owe it to yourself to check it out. If you’re a fan of compelling characters, interesting plot, and superb writing, you also owe it to yourselves.
The Waves Arisen by wertifloke
Fantastic and compact Naruto rationalist fic that does about as much to the story and world as what HPMOR did to Harry Potter. Definitely worth reading if you’re a Naruto fan, and may even be worth reading if you’re not.
Original Web Fiction
Worm is, simply put, the best superhero story I’ve ever read. Amazing worldbuilding, characters, plot, fight scenes, powers, everything you could ever want in a realistic “cape” story that I enjoyed even more than any from the Marvel or DC universes. Much like The Wire ruined cop shows in general, while Worm didn’t quite make other superhero stories unwatchable, it did render them difficult to take as seriously.
Imagine if the God of the Old Testament was real, and speaking parts of his True Name (in Hebrew of course) let you cast magic spells. Then imagine corporations patented parts of the Name to monopolize their use, and were resisted by an underground coalition of Unitarian Universalist communist kabbalists. Then imagine the whole thing was written like a cross between Douglas Adams and Good Omens.
It’s pretty fantastic, is what I mean to say.
There’s not much to say about this short story other than that it accomplishes what sci-fi does best, using improbable situations and compelling plots to hold a mirror up and help us to examine ourselves, our beliefs, and the very essence of what it means to be human.
One of the more unique magic systems I’ve come across, where every human has a power over a specific element or substance or idea, and the only way to get stronger with it is to gain fame. This leads to characters and a plot that is wonderfully meta in its examination of what it means to be a hero or villain, and the motivations that lead people to power and influence how they use it.
Mother of Learning by nobody103
Wonderfully well constructed caught-in-a-time-loop story with a familiar yet original fantasy world and magic system. The protagonist’s approach to improving himself and solving the mysteries of the situation he finds himself in are well thought out and executed, while still containing enough mistakes and setbacks and unexpected surprises to keep things entertaining.
A Practical Guide to Evil by ErraticErrata
This is probably one of the downright “funnest” stories I’ve read that don’t quite veer into a comedic genre the way something like Unsong does. Its world and characters are fantastically constructed, and the premise is both original and gripping: the world is full of Heroes and Villains that are granted Roles based on their background and skills, and the author holds nothing back in making the protagonist an actual Villain rather than just an anti-Hero or similar, while still managing to keep her sympathetic. The closest thing can compare the writing to is The Dresden Files, which is one of the highest compliments I can give.