In the original print version, there was a small section of bookkeeping dedicated to explaining how to use the various locked and keys to proceed via suggested routes. Most of this is currently handled by browser-tracked variables, so simply know that in some chapters you will find a "key". This "key" will later allow you to open a "lock" and read an otherwise unavailable chapter. Only by reading and collecting keys to unlock chapters can you hope to read most of the story.
To play, read a chapter. At the end of the chapter will be one or more links, giving options of which chapter to read. You can pick any of them, assuming you have the appropriate key if the path is locked. Locked paths are always clearly marked. Eventually, you will reach an ending. You may find a key you have no use for, but be aware that these keys carry over into the next reading, so that you can choose new paths.
The most important rule, however, is that you must cheat. If you only read as the links tell you, you will never see the whole story. Some links move backwards and other chapters don't have links to them at all. By using the checklist to see what you've read and the map to see where you can go, you can pick chapters to read (there are links in the table of contents) when you might otherwise not be able to.
There are many possible endings you will encounter as you read, but only one final and true ending. The others represent the way things could have gone, alternate realities where things fell apart a little bit differently, but it's up to you to track down the true ending.
Memento Mori is intended to be a somewhat unique gamebook in that in can be read and played in any order or fashion the reader wishes while still maintaining the same message (although there is no arguement that it makes linear sense regardless of how it's read).