Beginner Javascript course - recommended books
A great resource to learn JavaScript is Eloquent JavaScript by Marijn Haverbeke: https://eloquentjavascript.net/.

You can download the pdf for free, or you can read it online, and this is probably a better choice since you can take advantage of the code sandbox.

It is definitely suitable for beginners but a wide range of topics is covered, included Node.js (chapter 20). However, with regards to your requests, HTML and CSS are introduced but you will probably need supplementary material about them.