In 1717, Bonnet attacked a brigantine from Boston and a Barbadian sloop off North Carolina, and he used the Barbadian sloop to repair his own ship. In September 1717, as a result of a fight with a Spanish Navy man o' war while en route to Nassau, Revenge was heavily damaged, Bonnet was seriously wounded, and he lost half of his crew. At Nassau, he repaired his ship and increased its armament to twelve guns. The wounded Bonnet gave the famed pirate Blackbeard control of his ship, and he remained a guest on the ship until he recovered. In September 1717, the ship plundered a ship full of Madeira wine in Delaware Bay, and the ship plundered the ships Spofford and Sea Nymph as they left port in Philadelphia, Pennsylvania. On 22 October 1717, Revenge robbed the Robert and Good Intent of their supplies. In November, the ship returned to the Caribbean, and Blackbeard would seize the ship Concorde, which he renamed Queen Anne's Revenge and made his flagship. In December 1717, Bonnet and Blackbeard parted ways, but Bonnet was forced to rejoin Blackbeard when his crew deserted him, and he did not command the Revenge again until the summer of 1718.
In North Carolina, Governor Charles Eden gave both Blackbeard and Bonnet the King's pardon, and Bonnet was permitted to go to Saint Thomas to become a privateer for Denmark. Bonnet's crew was again stolen by Blackbeard, who also took many of his supplies, so Bonnet rescued some of Blackbeard's former sailors after they were stranded when the Queen Anne's Revenge was beached. Bonnet was forced to nullify his pardon due to Blackbeard stealing all of his food and Saint Thomas being caught in a hurricane, as Bonnet needed food and money. He renamed his ship to Royal James (due to his and his men's Jacobite sympathies) and began calling himself "Captain Thomas" in hopes of preserving his pardon, but he later quit his charade after robbing two ships. In July 1718, Bonnet pillaged eleven vessels in the Chesapeake Bay, pressing many prisoners into his crew. He kept the prize sloops Francis and Fortune after capturing them, letting the other ships go, and he was forced to make anchor in the Cape Fear River of North Carolina after his ship began to leak. The British sent ships from Charleston, South Carolina to put an end to Bonnet's piracy, and two British merchant sloops under William Rhett defeated Royal James, Francis, and Fortune from 26 to 27 September 1718. Bonnet was captured, and he managed to escape before being imprisoned again. His mental deterioration led to many pitying him, especially the women of the Carolinas, and the governor delayed his execution seven times. However, he was finally hanged on 10 December 1718 in Charleston.