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A short alternative to this guide is available here.
This guide is written to help people teach themselves japanese in an effective way. There's a lot of bad advice out there. This guide is specifically taking stances on a lot of important decisions so that you don't have to. This guide will tell you what to do to learn japanese, what you're in for, and explain some japanese language related trivia in the process.
Japanese is a human language. Every human learns language in one way and only one way: by consuming and understanding it. In general, you don't actually acquire a grammar feature by memorizing it from a textbook, but by seeing it used so much that you just know it. Nothing else works.
Of course, it's still better to start easy and work your way up in difficulty. And because japanese has exactly zero real cognates with languages that didn't borrow heavily from chinese, it's harder to break your way into simple natural material without preparation. But the goal at the end of the day is to go through japanese media and understand it, because nothing else will actually let you acquire the language.
Japanese takes a very long time to learn. If you don't need to generally acquire the language, and only need to pass a specific test or know enough to get around on the streets for a month, focusing on those specific goals will bring you to them earlier. You'll just know less real japanese. This entire guide focuses on real japanese, not specific unnatural usecases of it.
You will read a grammar guide. Not to memorize it. Not to test yourself. Not to fill out a curriculum. You're going to read the grammar guide to prime your brain on the differences between japanese and english. And to put grammar features into your head, so when you see them when reading or listening, you can identify them more easily and acquire them more easily. The grammar guide can't teach you japanese, it can only prepare you for acquiring it.
Do not stay with your beginner guide forever. There's no point to it. You won't master it without going beyond it, even if you try. Just read it and get over it and move on with learning more japanese.
The overwhelming majority of your grammar knowledge will come from reading in japanese. Nobody in the world, not even the best linguists, can do more than scratch the surface of how grammar works. It's just not possible. It's too complex, there are rules nested deep within rules and we don't even know the way they're represented in the human mind. Just read.
Tae Kim's Japanese Grammar Guide - A free grammar guide designed for self-learners. Full of problems, but still better than everything else. Everything in Tae Kim is basic grammar, including the advanced sections. The "Complete Guide to Japanese" is incomplete and badly structured, do not use it.
Note that Tae Kim does not have native-level japanese and is not a linguistician; the "focus particle" rant should be ignored completely because it's misleading. When something doesn't make sense, defer to Visualizing Japanese Grammar, or to a dictionary/handbook like A Dictionary of Japanese Grammar or A Dictionary of Japanese Particles.
Visualizing Japanese Grammar - Video explanations of japanese grammar concepts, made by a japanese linguist. Very good supplement to Tae Kim, but because of its structure, not recommended as a primary source of grammar.
Let's Learn Japanese I & II aka Yan and the Japanese People - Public broadcast series. Actually very good. Contains everything needed to teach you the basic spoken japanese language. Highly recommended, the only flaw is being in video format.
Imabi - Not recommended. While the advanced sections are a useful reference, the beginner material is riddled with extremely hard-to-understand, badly-written english, and is so unnecessarily dense that it's basically incomprehensible even if you know what it's saying. The author says they're working on rewriting the beginner material, but don't bother with it unless they do.
College Textbooks - Not recommended. These are long-winded and expect you to master the material, which is bad. They usually explain japanese grammar out-of-order, and contain things that don't make sense for self-learners like exercises. If you absolutely have to use one, use Genki I & II.
You will memorize the hiragana and katakana (explained later). This can take anywhere from a week to two months, depending on how your brain works. This should be done at the same time as reading your grammar guide, because the grammar guide will use hiragana and katakana, giving you extra exposure and making them easier to remember.
You will acquire vocabulary. You can do this in any way you want. You can memorize vocabulary with flashcards, you can acquire vocabulary while talking to people (easy, but very time consuming), you can read up on single words whenever you see them and remember them that way, you can read real japanese and fill in the blanks with your reading comprehension and figure out what words mean.
It doesn't matter how you acquire vocabulary as long as you do, but some methods are absolutely slower than others. The fastest method is memorization, but it's very stressful. The most efficient method is natural acquisition through reading comprehension, which is relatively fast and relatively low stress, and results in higher quality acquisition than memorization. In fact, most people both memorize words and acquire them when naturally reading.
Acquiring vocabulary from conversation and incidental studying are sure-fire methods, but are very slow, and are not recommended. Note that memorization can be really hard if your brain still thinks kanji look like scribbles, and in that case, you might want to learn the "radicals", or put kanji information in your vocab flashcards.
Finally, you will read. This will begin after memorizing the hiragana, but at the same time as reading the last parts of your grammar guide and whatever additional vocabulary learning methods you choose.
The best media to read for learning are Manga and Visual Novels.
Manga have both verbal and visual storytelling, so your comprehension of the material will be very high, which is necessary for easy acquisition of grammar and words. A lot of manga have "furigana", which makes acquiring "kanji vocabulary" easier, and makes dictionary lookups easier.
Visual Novels contain digital text and usually have voiced dialogue. Digital text means that you can use programs called texthookers, which make digital dictionary lookup very easy. This dramatically increases the level of japanese you can work your way through understanding every word. The spoken language is the actual language, so exposing yourself to spoken dialogue is a must.
Japanese uses four scripts: The latin alphabet, two syllabaries called the hiragana and katakana, and logographic characters from china called kanji.
The kana are syllabaries. This means that each character refers to a sequence of sounds, and each character's shape is basically irregular. The hiragana come from heavily simplified cursive kanji, and look scribbley. The katakana come from cutting glyphs out of kanji, and look square.
Hiragana is primarily used for everything that isn't written in kanji. Katakana is primarily used for writing special words like loanwords or words where the kanji has to be omitted, or to indicate weird sounds like a dialect or onomatopoeia.
This is a very general distinction. The preference definitely goes to hiragana, and hiragana is absolutely the syllabary you should focus on first.
You can learn to write the kana, but it's not necessary at all.
You can train your kana knowledge here.
The great equalizer. Kanji is, as stated earlier, a set of logograms (word-letters) borrowed from china. Unlike china, where hanzi map directly to words or halves of words, kanji map to general morphemes. A morpheme is the smallest bit of a word that has individual meaning. In "unrestful", the morphemes are "un", "rest", and "ful".
You're discouraged from learning to write all the kanji. It's extremely time consuming. You can learn to write some basic characters, the general rules behind stroke order, and how kanji composition works, in fact it's a good idea to. But memorizing how to write every single kanji individually is very time consuming, and should be avoided until you're adept at japanese.
Japan had its own words before it adopted kanji from china. And japan decided to assign kanji to those native words. Japanese even assigns the same kanji to different native words, and only notes the difference with gloss text showing pronunciations (called furigana) or with extra hiragana sticking off the ends of the kanji, indicating which word it is. The pronunciations, or readings, of these native words with kanji, are called kun'yomi (ku-n-yo-mi, as opposed to kunyomi ku-nyo-mi).
Also, japan borrowed kanji from china during many different periods of chinese history, and in many different places which had slightly different uses of the hanzi. And when loaning them, the readings were changed to match the dialect of whatever japanese people were learning that kanji for the first time. So even among just the readings loaned from china (called on'yomi), there's often several for each kanji. In fact, these different readings have different nuances and meanings, and learning them out of context is more of a hassle than a help.
Japanese uses fewer kanji than china uses hanzi. 2136 are taught in school, but between 2300 and 3000 are used in actual media, depending on the media's demographic. The important part is to remember that this isn't "2000 things to memorize before I can start reading". It's "2000 ways to spell words that I'm going to know by the time I learn enough vocabulary". Kanji is an orthography, and treating kanji as something other than a way to write words would only stress you out and make things take longer.
You can view a list of chinese kanji reading groups here. Don't bother memorizing it, it's just to help you wrap your head around things.
Radicals are the component graphemes that kanji are organized by in traditional paper dictionaries. Radicals have etymological meaning like "water" or "going a long distance", but you can't accurately tell the meaning of a kanji from its radicals. That being said, radicals are still a great place to start to make your brain think kanji don't look like scribbles, and are easier to learn than the kana (at least after you learn the kana).
Wanikani is highly discouraged because it's very expensive, and RTK is highly discouraged because it's very hard to use in an efficient way. There are good kanji resources, but the important thing is that, if you use them, you only use them to supplement your studies, not to replace vocab study or reading. Kanji study doesn't teach you japanese, it only makes it easier to learn words. Better yet, don't use a kanji resource if it doesn't teach you vocabulary.
Manga and VNs are highly recommended. The easiest good manga with furigana is Zettai Reiiki. The easiest visual novel is Hanahira, but it's widely considered very boring.
There's a "reading pack" for the manga Yotsubato!, which is basically a bundle of a vocabulary list and anki deck, available here. If you're really lazy, using this and reading Yotsuba might be what you want, even though Yotsuba isn't as easy as Zettai Reiiki.
A partial transcript of Sayonara Zetsubou Sensei is available here. SZS is extremely relatable, and might be the way for you to go if Zettai Reiiki and Yotsuba are just not compelling.
Several visual novel recommendation charts can be found here. The best VN recommendation charts for people learning japanese are these three: 2 - 4 - 6. In general (but not always), an absolute beginner's first VN should be something with a difficulty of 1 or 2, as defined on the VN Difficulty Measuring Stick. Basically, the dialogue and narration shouldn't stray far from the spoken language, because the written language is more unbalanced, nuanced, and difficult to naturally acquire words and grammar from. After your very first VN, you can read whatever you want, even something hard like Dies Irae.
If you're reading VNs, you're going to want a texthooker. You can find the latest version (as of 2017-03-17) of the best texthooker here. View these instructions for information on how to use a digital dictionary with ITHVNR.
Do not use machine translation, not even to "make sure you understand things", and also do not use parsers if they don't let you fix their mistakes (for example, chiitrans lite doesn't allow you to fix its mistakes).
Memorization means that anyone can learn anything, even if they don't understand it. But memorizing by going down a list and writing it over and over again is very inefficient. Luckily, people figured out that you can just show yourself things you know better less often, and that's maximally efficient. This is called spaced repetition, and most spaced repetition takes the form of flashcards.
The premier spaced repetition flashcard program is Anki. Anki is open source software on desktop. Ankidroid is an unofficial-but-approved open source Anki clone. Anki iOS is an official but commercial Anki client for iOS. Ankiweb is an official free-of-cost web client for anki. You have to use at least one of the non-web clients on a somewhat regular basis, because Ankiweb is not fully functional.
You can get good anki decks here, which are generally better than the popular decks on anki's shared decks website. Note that "recognition" cards, as in the front being something unknown, and the back being something known, are less time consuming than "recall" cards, as in the front being something known, and the back being something foreign. Don't even bother with "exposure" cards, where everything is on the front.
Read this image. Follow its advice. You absolutely have to raise the "Maximum reviews/day" setting to at least 200. You absolutely have to uncheck the "Bury related reviews until the next day" button.
The best way to learn vocabulary is to memorize it at the same time as acquiring it from real material. You can kill two birds with one stone by "mining" vocabulary from what you read, putting it in a flashcard, and memorizing that flashcard in anki. After some configuration, this is easier to do with visual novels than anything else, just follow these instructions or these instructions.
You can mine absolutely anything, including manga or anime. There are specialized guides for mining from anime available on the internet. In general, if you can make a list of words, definitions, and sentences, separated by tabs, in a text file, you can import that into anki. That's how mining works.