The first book is a series of flashbacks from 1713 to the earlier life of Daniel Waterhouse. It begins as Enoch Root arrives in Boston in October 1713 to deliver a letter to Daniel containing a summons from Princess Caroline. She wants Daniel to return to England and attempt to repair the feud between Isaac Newton and Gottfried Leibniz. While following Daniel's decision to return to England and board a Dutch ship (the Minerva) to cross the Atlantic, the book flashes back to when Enoch and Daniel each first met Newton. During the flashbacks, the book refocuses on Daniel's life between 1661 and 1673.
While attending school at Trinity College, Cambridge, Daniel becomes Newton's companion, ensuring that Newton does not harm his health and assisting in his experiments. However, the plague of 1665 forces them apart: Newton returns to his family manor and Daniel to the outskirts of London. Daniel quickly tires of the radical Puritan rhetoric of his father, Drake Waterhouse, and decides to join Reverend John Wilkins and Robert Hooke at John Comstock's Epsom estate.
There Daniel takes part in a number of experiments, including the exploration of the diminishing effects of gravity with changes in elevation, the transfusion of blood between dogs and Wilkins' attempts to create a philosophical language. Daniel soon becomes disgusted with some of the practices of the older natural philosophers (which include vivisection of animals) and visits Newton during his experiments with color and white light. They attempt to return to Cambridge, but again plague expels the students. Daniel returns to his father; however, his arrival on the outskirts of London coincides with the second day of the Fire of London. Drake, taken by religious fervour, dies atop his house as the King blows it up to create a fire break to prevent further spread of the fire. Soon after Drake's death, Newton and Daniel then return to Cambridge and begin lecturing.
A flashforward occurs in the narration, to find Daniel's ship under attack by the fleet of Edward Teach (Blackbeard) in 1713. Then the story returns to the past as Daniel and Newton return to London: Newton is under the patronage of Louis Anglesey, the Earl of Upnor, and Daniel becomes secretary of the Royal Society when Henry Oldenburg is detained by the King for his active foreign correspondence. During his stint in London, Daniel encounters a number of important actors from the period. Daniel remains one of the more prominent actors in the Royal Society, close to Royal Society members involved in court life and politics. By 1672 both Daniel and Newton become fellows at Trinity College where they build an extensive alchemical laboratory which attracts other significant alchemists including John Locke and Robert Boyle. Daniel convinces Newton to present his work on calculus to the Royal Society.
In 1673, Daniel meets Leibniz in England and acts as his escort, leading him to meetings with important members of British society. Soon, Daniel gains the patronage of Roger Comstock as his architect. While under Roger's patronage, the actress Tess becomes Daniel's mistress both at court and in bed. Finally the book returns to 1713, where Daniel's ship fends off several of Teach's pirate ships. Soon they find out that Teach is after Daniel alone; however, with the application of trigonometry, the ship is able to escape the bay and the pirate band.
The King of the Vagabonds
The King of Vagabonds focuses on the travels of "Half-Cocked" Jack Shaftoe. It begins by recounting Jack's childhood in the slums outside of London where he pursued many disreputable jobs, including hanging from the legs of hanged men to speed their demise. The book then jumps to 1683, when Jack travels to the Battle of Vienna to participate in the European expulsion of the Turks. While attacking the camp, Jack encounters Eliza, a European slave in the sultan's harem, about to be killed by janissaries. He kills the janissaries and loots the area, taking ostrich feathers and acquiring a Turkish warhorse which he calls Turk. The two depart from the camp of the victorious European army and travel through Bohemia into the Palatinate. To sell the ostrich feathers at a high price, they decide to wait until the spring fair in Leipzig. Jack and Eliza spend the winter near a cave warmed by a hot water spring. In the springtime, they travel to the fair dressed as a noblewoman and her bodyguard where they meet Doctor Leibniz. They quickly sell their goods with the help of Leibniz, and agree to accompany him to his silver mine in the Harz Mountains.
Once they arrive at the mine, Jack wanders into the local town where he has a brief encounter with Enoch Root in an apothecary's shop. Jack leaves town but gets lost in the woods, encountering pagan worshippers and witch hunters. He successfully escapes them by finding safe passage through a mine connecting to Leibniz's. Eliza and Jack move on to Amsterdam, where Eliza quickly becomes embroiled in the trade of commodities. Jack goes to Paris to sell the ostrich feathers and Turk, leaving Eliza behind. When he arrives in Paris, he meets and befriends St. George, a professional rat-killer and tamer, who helps him find lodging. While there, he becomes a messenger for bankers between Paris and Marseilles. However, during an attempt to sell Turk Jack is captured by nobles. Luckily, the presence of Jack's former employer, John Churchill, ensures that he is not immediately killed. With Churchill's help, Jack escapes from the barn where he has been held prisoner. During the escape, he rides Turk into a masquerade at the Hotel d'Arcachon in a costume similar to that of King Louis. With the aid of St. George's rats he escapes without injury but destroys the ballroom and removes the hand of Etienne d'Arcachon.
Meanwhile, Eliza becomes heavily involved in the politics of Amsterdam, helping Knott Bolstrood and the Duke of Monmouth manipulate the trade of VOC stock. This causes a panic from which they profit. Afterwards, the French Ambassador in Amsterdam persuades Eliza to go to Versailles and supply him information about the French court. Eliza agrees after a brief encounter and falling-out with Jack. William of Orange learns of Eliza's mission and intercepts her, forcing her to become a double agent for his benefit and to give him oral sex. Meanwhile, Jack, with an injury caused by his encounter with Eliza, departs on the slaving trip, the ship filled with cowry shells which he and his accomplices, a Russian fur trader and an English pub owner. The ship is captured by Barbary pirates, and the end of the book has Jack as a captured galley-slave.
This book returns to Daniel Waterhouse, who in 1685, has become a courtier to Charles II because of his role as Secretary of the Royal Society. He warns James II, still Duke of York, of his brother Charles' impending death, following which, Daniel quickly becomes an advisor to James II. He continues to be deeply involved with the English court, ensuring the passage of several bills which reduce restrictions on non-conformists despite his detraction from the Francophile court. Meanwhile, Eliza becomes the governess of a widowers' two children in Versailles. She catches the eye of the king and becomes the broker of the French nobility. With her help, the French court, supported by King Louis, creates several market trends from which they profit extensively. Her active involvement in the French court gains her a title of nobility: Countess of Zeur.
Daniel and Eliza finally meet during a visit to the Netherlands where Daniel acts as an intermediary between William of Orange and the detracting English nobility. Daniel realizes Eliza's importance during a meeting at the house of Christiaan Huygens. Eliza woos Daniel and uses this connection to gain entrance into the English court and the Royal Society. Daniel also meets Nicholas Fatio while in Amsterdam. Soon after this meeting, Fatio and Eliza prevent the attempted kidnapping of William of Orange by an ambitious French courtier. Upon his return, Daniel is arrested by the notorious judge George Jeffreys, and later imprisoned in the Tower of London. Daniel escapes with the help of Jack Shaftoe's brother Bob, whose infantry unit is stationed there.
After a brief return to Versailles, Eliza joins Elizabeth Charlotte of the Palatinate at her estate before the invasion of the Palatinate in her name. Eliza informs William of Orange of the troop movements caused by the French invasion which frees his forces along the border of the Spanish Netherlands, a region of stalemate between France and the Dutch Republic. During her flight from the Electorate of the Palatinate, Eliza becomes pregnant by Louis's cryptographer, though popular knowledge suggested it was the French nobleman Etienne D'Arcachon's child. Meanwhile, William takes the free troops from the border on the Spanish Netherlands to England, precipitating the Glorious Revolution, including the expulsion of James II. James flees London and Daniel Waterhouse soon encounters him in a bar. Convinced that the Stuart monarchy has collapsed, Daniel returns to London and takes revenge on Jeffreys by inciting a crowd to capture him for trial and later execution. Though he plans to depart for Massachusetts, Daniel's case of bladder stones increasingly worsens during this period. The Royal Society and other family friends are very aware of this and force Daniel to get the stone removed by Robert Hooke at Bedlam.