Slightly more work answer: Python + Scrapy
With python & scrapy you can fetch the web pages that you need, separate out the content from the other information, possibly also fetch other information linked from within the story, and collate it as you wish, there are lots of examples on the website & on stackoverflow.
Python can even create the ebook for you directly - either using just the standard libraries, (again there are examples on the web of how to do this), or with the ebooklib.
- Price: Free
- Output formats: Any you care to implement
- Platform: Windows/OS-X/Linux/RaspberryPi/lots of others
- Add ToC Option: Yes
- Work for you to do: Learn some python & scrapy, identify the web page sections that you need, write & test the scripts.
This approach is more work than my other answer and does not do the job out of the box but will eventually produce a better looking final result and you will learn a lot of transferable skills.
Of course you should check the author(s) of the web pages permissions/licence terms before using this to make sure that it is an allowed usage