The Confusion is the second volume of Stephenson's "Baroque Cycle" and encompasses books four and five of the story. Book four is titled "Bonanza" and concerns the travels and travails of Jack Shaftoe aka The Vagabond King, aka Half-cocked Jack. Jack awakens from a syphilitic stupor to find himself a galley slave. He and fellow slaves conspire to steal a ship which turns out to be laden with gold and run afoul of the duc D'archchon who bears a murderous grudge against Jack. The action in this part takes Jack to India, Japan, and eventually back to Europe. Told in alternate sections with "Bonanza" is book five, "The Juncto", which concerns Eliza and her machinations in the conflicts between William of Orange and the Jacobites and later James II. Eliza suffers the loss of her fortune, the kidnapping of her illegitimate son, smallpox, and the death of her husband, regaining her fortune, and more. The other main character of "The Juncto" is Bob Shaftoe, brother of Jack, and his participation in war between William and James on the side of William. There are also appearances by Daniel Waterhouse, Isaac Newton, Gottfried Leibniz, and others who featured heavily in volume one.
