Check out "Tae Kim Japanese Grammar" if you want to learn Japanese in a way that makes intuitive sense.
That guide is great because it truly starts with the foundations, so you always know exactly what you are doing.
It uses tons of example phrases to really show how things work in actual writing, and it takes one step at a time at a pleasant pace.
Actually, I might as well link you to that site:
http://www.guidetojapanese.org/learn/grammar
I think "Table Of Contents" has all the information you will ever need.
It might look like a lot, but each section gets you closer and closer to understanding the language.
Just focus on one topic at a time and it will feel much more manageable.