www.makemkv.com

I bought the boxed version of Vikings and am backing that up before watching anything. It seems like MakeMKV is the only way to get the chapters out since there is no one large file to choose from.
When opening the files with MakMKV, I can see several episodes per disc. Do I need to save each episode individually or will MakeMKV separate all the episodes if all are selected at once?

If they show up separately in MakeMKV, they’ll be separate files after ripping.

Yes, each "Title" that is "checked" in MakeMKV will produce an .mkv file.

Assuming we're talking about a Blu-ray or UltraHD disc:

If there's a "PLAY ALL" playlist (.mpls) checked, then you will get a file with all episodes playing one-after-the-other, and all the chapters for all the episodes should also be within that file (depending on how the playlist was structured, of course).

You would normally determine whether a .mpls title is "PLAY ALL" by the segment map. If there's five episodes on each disc, you may see a segment map like "1,2,3,4,5", which corresponds to the files 00001.m2ts, 00002.m2ts, 00003.m2ts, 00004.m2ts & 00005.m2ts (leading zeroes always get dropped from segment maps).

If you also see a .mpls title with a segment map of "1" then you know that is the first episode by itself, another .mpls title with a segment map of "2" is the second episode, and so on. "PLAY ALL" files are a great way to determine which order the episodes are in on the disc, as they aren't always numbered sequentially.

If you're working from a decrypted backup of the disc, you can also navigate to the BDMV/STREAM/ folder and play each of those transport streams (.m2ts files) directly using VLC Media Player, which may also help to verify what the content is.

Please note that those file names I mentioned above are just an example. However the files are named is up to whoever authored the disc. A five-segment map may look like "50137,32,966,43768,807", it's just a list of files (ie. "segments") to play in a certain order.

You may then have a choice of ripping the "PLAY ALL" playlist title, or the individual episode playlist titles, or if all else fails, the individual episode transport streams (.m2ts), except transport streams don't have chapters so treat that as a last resort.

If we're talking about a DVD then that's a whole different kettle of fish. DVD titles can have segments but they don't relate to file names like a Blu-ray does, I think they relate to "cells" or something like that.

Although DVDs can still have "PLAY ALL" titles and individual episode titles without doubling-up on the physical data by each one accessing the same "cells", you can't cross-reference one title to another like you can on a Blu-ray.