The boxes contain the miniatures, bases, and the stat cards. The rules come in 1 of 2 books, Malifaux 1.5, which has all the fluff from book 1, and all of the updated rules for the game and the models that were listed in book 1. The Rules Manual is 15 dollars, it's small, and it's rules are only slightly out of date. All of the basics are there, it's just missing some clarifications. It also has no model rules or fluff.
You can get the Rules Manual in an edited PDF (it's got a bunch of extra artwork in it that covers up some diagrams), but it's free, it's available, and it has all of the rules to play.
Fate decks are nothing more than a deck of cards with 2 jokers in it. They are sold separately, but you can get around buying the fate deck if you just use a standard deck of cards. They also have a free cheat sheet on their website that has the conversions from normal card suits to Mailfaux suits.
See this thread for more info:
http://www.dakkadakka.com/dakkaforum/posts/list/474150.page