Last year /u/Starwarsnerd222 fulfilled a similar request

Brett L. Walker's Concise History of Japan or Nancy Stalker's Japan: History and Culture from Classical to Cool are usable survey textbooks written with beginner, undergrad students in mind. I'd start here. But it doesn't matter too much what the first book of this kind is that you'll read since they all have to compress things so much, and they will inevitably not reflect our current state of knowledge on all the topics they breeze through. It's there to provide you with a first, general roadmap to place puzzle tiles that more in-depth readings will offer to you.

After that, just dive into whatever topics happen to fancy your interest. (Of course, feel free to come back and ask for reading recommendations if you feel lost again!)

For example, if you want to learn about samurai, you could also take a look at Michael Wert's Samurai: A Concise History, which is cheap, short, and pretty decent. (I didn't hate the Kamakura chapter, which is rare.)

Also, there are a lot more books only focusing on modern Japan, omitting the interesting part (hehe), which I'm not going to bother list unless you are particularly interested in more recent history. They, of course, also tend to be more in-depth since they are much more narrow.