Below is a link to a very good Tutorial made by LearnWebCode on YouTube that teaches you how to make your own WordPress Theme as well as explains what each individual page does and the purpose of the .php file . It’s what I watched when I first started off making my own WordPress Themes.
WordPress Theme Development – Tutorial
Regarding your question however – there are many different things you can put in the index.php file it all depends on how many other .php files you have.
Good luck,
Stephen 🙂