Later Stages, 1644–46
During the second half of the war, political opposition within the Royalist senior leadership against Rupert continued to grow. Rupert's personality during the war had made him both friends and enemies. He enjoyed a "frank and generous disposition", showed a "quickness of... intellect", was prepared to face grave dangers, and could be thorough and patient when necessary. However, he lacked the social gifts of a courtier, and his humour could turn into a "sardonic wit and a contemptuous manner": with a hasty temper, he was too quick to say who he respected, and who he disliked. The result was that, while Rupert could inspire great loyalty in some, especially his men, he also made many enemies at the Royal court. When he took Bristol, he also slighted the Marquis of Hertford, the lethargic but politically significant Royalist leader of the South-West. Most critically, Rupert fell out with George Digby, a favourite of both the King and the Queen. Digby was a classic courtier and Rupert fell to arguing with him repeatedly in meetings. The result was that towards the end of the war Rupert's position at court was increasingly undermined by his enemies.
Rupert continued to impress militarily. By 1644, now the Duke of Cumberland and Earl of Holderness, he led the relief of Newark and York and its castle. Having marched north, taking Bolton and Liverpool along the way in two bloody assaults, Rupert then intervened in Yorkshire in two highly effective manoeuvres, in the first outwitting the enemy forces at Newark with speed; in the second, striking across country and approaching York from the north. Rupert then commanded much of the royalist army at its defeat at Marston Moor, with much of the blame falling on the poor working relationship between Rupert and the Marquis of Newcastle, and orders from the King that wrongly conveyed a desperate need for a speedy success in the north.
In November 1644 Rupert was appointed General of the entire Royalist army, which increased already marked tensions between him and a number of the King's councillors. By May 1645, and now desperately short of supplies, Rupert captured Leicester, but suffered a severe reversal at the Battle of Naseby a month later. Although Rupert had counselled the King against accepting battle at Naseby, the opinions of Digby had won the day in council: nonetheless, Rupert's defeat damaged him, rather than Digby, politically. After Naseby, Rupert regarded the Royalist cause as lost, and urged Charles to conclude a peace with Parliament. Charles, still supported by an optimistic Digby, believed he could win the war. By late summer Rupert had become trapped in Bristol by Parliamentary forces; faced with an impossible military situation on the ground, Rupert surrendered Bristol in September 1645, and Charles dismissed him from his service and command.
Rupert responded by making his way across Parliamentary held territory to the King at Newark with Prince Maurice and around a hundred men, fighting their way through smaller enemy units and evading larger ones. King Charles attempted to order Rupert to desist, fearing an armed coup, but Rupert arrived at the royal court anyway. After a difficult meeting, Rupert convinced the King to hold a court-martial over his conduct at Bristol, which exonerated him and Maurice. After a final argument over the fate of the governor of Newark, who had let Rupert into the royal court to begin with, Rupert resigned and left the service of King Charles, along with most of his best cavalry officers. Earlier interpretations of this event focused on Rupert's concern for his honour in the face of his initial dismissal by the King; later works have highlighted the practical importance of the courts martial to Rupert's future employability as a mercenary in Europe, given that Rupert knew that the war by this point was effectively lost. Rupert and Maurice spent the winter of 1645 in Woodstock, examining options for employment under the Venetian Republic, before returning to Oxford and the King in 1646. Rupert and the King were reconciled, the Prince remaining to defend Oxford when the King left for the north. After the ensuing siege and surrender of Oxford in 1646, Parliament banished both Rupert and his brother from England.