It's a 'checkpoint' system. Save game or not, the game is constantly checking with Ubisoft's servers - if it can't talk to them it just boots you out. The save thing is a bit of a red herring.
How does that work though? Can't the points where that check is called just be hex-edited to NOOP in the binary? The point of the article was that taking non-trivial portions of the game logic out of the game and pushing them to the server makes it harder to crack the system. Unless the game is constantly getting information from Ubisoft's servers that it needs to function (i.e. save-game logic, AI logic, etc), then the "verify with the server" code can just be ignored in a hacked binary.
