How about Jules Verne's “The Mysterious Island”?

It doesn't have any “rationality ninjas”, but the overall arch of “know your world, understand it, and force your will upon your future” seems a very valuable basis of thought for any rational person. This book was probably the most powerful root of that idea in my mind.

As a bonus, pretty much everything the characters do would actually do work in real life.

(Actually, quite a few other stories by JV are really nice. This one is just the one most tightly connected in my mind with the basic idea of reason.)