Well, what you have to understand is that the JLPT test is explicitly a test for non-native learners of the language, and the way a second-language learner studies a language is never going to be identical to that of a native speaker. Yes, native speakers "study"/"learn" their own language at school, too, but this typically means reading literature to improve critical reading skills, learning certain things about grammar to be able to fine-tune their understanding of how their native language works, et cetera and so forth. A native speaker already has a command of their own language far, far beyond that of a second-language learner long before they ever "study" their language in school.
So the long story short is, no, there is no single resource (in terms of a "school book") that will take you from the zero or early intermediate level as a second language learner to the equivalent of a native speaker. To be honest, even JLPT N1 (though it requires a demonstration of advanced proficiency in the sense of being able to read and answer questions about reading materials designed for native speakers, etc.) does not represent a "native's" level of understanding, and it is very possible to pass JLPT N1 (even with something very close to a perfect score) while still having a level of Japanese far, far below what anyone would consider as "native."
Speaking from personal experience, passing JLPT N1 on the road to developing a high (close to native) level of proficiency and fluency will often involve starting with a solid textbook (the Genki series is the most popular/most often recommended, though there are other good ones out there), which will probably get you up to about the JLPT N3 or so level. Then (either after you finish, or starting even earlier depending on your learning method), you'll be supplementing your studies with exposure to native materials (books/media/etc. made for native Japanese speakers) and using other reference materials to help you understand what you're reading. Eventually, you'll reach the JLPT N2/N1 level, at which point you should be fairly independent as a learner, "learning"/"studying" mostly by consuming materials made for native speakers, looking things up in Japanese-Japanese dictionaries (i.e. monolingual Japanese dictionaries made for native Japanese people), communicating to Japanese people in Japanese and getting occasional corrections (and doing self-correction), etc. etc.
Anyhow, I'm speaking mostly from my own experience. Everyone's experience is different, so you can take it with a grain of salt, but looking at other people I know who've reached a high level of Japanese proficiency, I would say most of the above is true for most of them. Textbooks are part of the process, but textbooks alone will not get you to that advanced/near-native proficiency level. And that's fine, really, because textbooks aren't really meant to do that (I would imagine this goes for learning any second language to a high level, though I personally only have experience with Japanese.)
I hope this helps to give a bit of perspective, and please let us know if you have any other questions!