Willis eventually became Colonel General of the counties of Lincolnshire, Nottinghamshire, and Rutland, and in May 1645 was appointed Governor of Newark. By this time Prince Rupert had been defeated at the Battle of Naseby, and through the machinations of Lord Digby, a rival and advisor to the King, came under suspicion as plotting against the crown. Rupert's subsequent surrender at Bristol caused Charles to dismiss his nephew from his service. While Charles was at Newark, Rupert arrived to confront him over what he considered the injury done to his honour; Willis rode out with Lord Gerard to greet him. The court-martial Rupert demanded exonerated him, but Willis, for what the King considered to be the disloyalty of his attendance on Rupert, was replaced by Lord Belasyse as Governor of Newark. Willis challenged him to a duel, but was stopped by the King; Rupert, his brother Prince Maurice, Gerard and other cavaliers took Willis's side and in the ensuing argument were all dismissed from the King's service.