This third installment in a saga picks up when Daniel Waterhouse, the protagonist, comes home from his technical education in Boston at college. He has been recruited to help discern through the conflict between Newton and Liebniz—both men famously invented calculus at the same time (in real life, yes) and when they delivered their math to the academy, they fought about who discovered it first. Before they can get to the bottom of the debate, a bomb explodes in an assassination attempt. The bomb turns out to have been an attempt on Newton's life. In an aside, we learn about Jack the Coiner and his heist of the London Tower.
Waterhouse and Newton go after Jack the Coiner because they suspect him of other nefarious dealings, and we learn about Princess Caroline and her helper Eliza. Princess Caroline is of the Hanovers and Eliza suspects these attacks might lead to an attempt to take her life in an attempt to undo the royal family. In the streets, the Whigs and Tories, political factions, take up arms against one another and do battle.
Before they can resolve the calculus debate, Newton dies of typhoid fever, but they use an alchemical stone from legend, the Philosopher's Stone, to resurrect Isaac Newton from the dead, because of the stone's divine magical qualities. Then, Jack the Coiner admits his wrongdoing and is hanged, but unbeknownst to most, he actually escapes to a life of privilege in the court of the famous French monarch, the lavish Louis XIV.