Perilous as was the condition of the Royalists on all sides, the condition of Wales seemed the most desperate, and thither Rupert hastened in the March of 1645. He took his way first to Ludlow, where he hoped to raise new forces, and a few days later he joined Maurice at Ellesmere. Thence he wrote despondently to Legge, dwelling on the great numbers of the enemy, and exhorting him to see that the Oxford army held Monmouthshire in check. "I am going about a nobler business," he added, "therefore pray God for me; and remember me to all my friends."[[36]] But by the 14th he had got an army together, and his spirits were marvellously revived. "We are few, but shrewd fellows as ever you saw. Nothing troubles us but that Prince Charles is in worse (condition), and pray God he were here. I expect nothing but ill from the West; let them hear that Rupert says so." (This was for Goring's benefit.) "As for Charles Lucas' business, assure the King that nothing was meant but that it should be conceded by Lord Hopton; but his lieutenant, Slingsby, is a rogue. I have enough against him to prove him so, when time shall be. This enclosed will show you a fine business concerning my cousin the Bishop of York. Pray acquaint His Majesty with it, it concerns him. Martin's man carried a letter to you from Stowe, which you did receive, and one for Sir Edward Herbert. Pray remember me to him, and to all my friends, and inquire about the letter; you'll find knavery in it. Prince Charles wrote to me about Mark Trevor; I denied it (i.e. refused) as well as I could: he goes to him. Cheshire will not prosper. (Maurice was there.) Your company is here, so is your friend Rupert."[[37]]

The allusion to the Archbishop of York shows that Rupert had already detected the intrigues of that warlike and treacherous prelate. He had fortified and defended his castle of Conway, but quarrelled incessantly with all the Royalist officers in the district, and eventually he admitted the enemy to his castle. At the date of the above letter he was following the example of Digby, and trying to sow dissension between Ormonde and Rupert. Cheshire and Wales, he declared, lay "all neglected and in confusion", owing to the private quarrels of Rupert's "favourite", Legge, and the Byrons, whom he represented as "thrown out of their governments, abandoned by the King, and left to die in prison."[[38]] The Byrons themselves do not appear to have made any such complaints; and a sentence in one of Lord Byron's letters to the Prince seems to deprecate the reports spread by the Archbishop. "I heard," he says, "that Your Highness was informed that, in your absence, I showed most disrespect to those you most honour. This is very far from the truth, as it ever shall be from the practice of your most humble and most obliged servant, Byron."[[39]]

And in spite of the Archbishop's hostility Rupert's efforts in the Marches were attended by success. On the 19th of April, having been rejoined by Maurice, he forced Brereton to raise his siege of Beeston Castle, which had endured for seventeen weeks. A few days later he was engaged in suppressing a revolt in Herefordshire, where the peasants were rising like the clubmen of Dorset. Most of them fled before the Prince, but two hundred stood their ground, of these Rupert took the leaders, and persuaded the rest to lay down their arms; he was anxious, if possible, to conciliate the people rather than to suppress them by force.[[40]] No sooner was this task accomplished than Astley arrived with the news that a Parliamentary force, under Massey, was at Ledbury. Without an instant's delay Rupert set out, marched all night, and attacked and routed Massey in the morning, April 22nd. From Ledbury he went to Hereford, where he remained some days before returning to Oxford.

It was at this time that Rupert performed the stern act of retaliation, which so roused the wrath of the Parliament. The King's importation of Irish soldiers had been regarded by the Puritans as a gross aggravation of all his other crimes. They chose to regard all the Irish as responsible for the massacre of the Protestants which had occurred in Ireland in 1641, and in accordance with this view they gave them no quarter. In March 1645 Essex happened to take thirteen Irish troopers, whom he hanged without mercy; and Rupert immediately retaliated by the execution of thirteen Roundhead prisoners. Essex thereupon wrote an indignant letter, reproaching the Prince for his barbarous and inhuman conduct, to which Rupert responded in a letter "full of haughtiness", that since Essex had "barbarously murdered" his men, "in cold blood, after quarter given", he would have been unworthy of his command had he not let the Puritans know that their own soldiers "must pay the price of such acts of inhumanity."[[41]] The Parliament then took upon itself to remonstrate at great length, but received only a concise and decided reply from the Prince's secretary:

"I am, by command, to return you this answer. You gave the first example in hanging such prisoners as were taken, and thereupon the same number of yours suffered in like manner. If you continue this course you cannot, in reason, but expect the like return. But, if your intention be to give quarter, and to exchange prisoners upon equal terms, it will not be denied here."[[42]] The Prince's resolute attitude had the desired effect, and the Puritans were forced to recognise Irishmen as human beings.

In contrast with this incident, we find a frantic appeal to the Prince for mercy, dated April 28. A young Royalist officer—Windebank—had most unjustifiably surrendered Blechingdon House, of which he was Governor, and by a court-martial held at Oxford he was doomed to die. Poor Windebank was no coward, but he had acted in a moment of panic, engendered by the terror of his young wife, and it was on his behalf that Sir Henry Bard now pleaded with Rupert. "The letter enclosed was sent to me from Oxford, to be conveyed with all speed possible. Pray God it comes time enough! It concerns a most unfortunate man, Colonel Windebank. Sir, pity him and reprieve him! It was God's judgment on him, and no cowardice of his own. At the battle of Alresford he gave a large testimony of his courage, and if with modesty I may bring in the witness, I saw it, and there began our acquaintance. Oh, happy man had he ended then! Sir, let him but live to repair his honour, of which I know he is more sensible than are the damned of the pains of hell."[[43]] Rupert had saved Fielding, and he would in all probability have saved Windebank had it been possible. But, alas, Bard's letter was intercepted by the Parliament and never reached its destination! And Windebank died on May 3rd, the day before Rupert reached Oxford.

The King was about to begin his last campaign, and he therefore summoned both his nephews to his side. The two Princes reached Oxford on May 4th, after an extraordinarily rapid march, and three days later, the King set out for Woodstock, leaving Will Legge behind him as Governor of Oxford. Danger was on every side. The Scots dominated the North; the West was falling rapidly away, and Cromwell's new army threatened that of the King. At starting, Charles had but 1,100 men, but before a month was past, Rupert had doubled their number. Digby and the Court party would fain have joined with Goring in the west, but Rupert, "spurred on by the northern horse, who violently pursued their desires of being at home,"[[44]] was eager for the North. For the moment his star was in the ascendant, and, to Digby's disgust, the King yielded. "All is governed by Prince Rupert who grows a great Courtier," reported Arthur Trevor. "But whether his power be not supported by the present occasion is a question to ask a conjuror. Certainly the Lord Digby loves him not."[[45]] At Evesham, which was reached on the 9th, Rupert gave new offence to the Court by making Robin Legge, Will's brother, Governor of that town, in defiance of the wishes of the Council. Moving slowly northwards through the Midlands, he took Hawkesly House near Bromsgrove; on the following day he was at Wolverhampton. On the 27th both he and the King were the guests of the Hastings, at Ashby de la Zouch, and on the 29th Rupert "laye in the workes before Leycester."[[46]] By his skill and energy, this town was taken in two days, and the triumph not only revived the drooping spirits of the Cavaliers, but won them material advantages in the way of arms and ammunition. It was believed that Derby would have surrendered on a summons, but Rupert would not take the chance. Should it refuse his summons, he maintained, "out of punctilio of honour" he would be forced to lay siege to it, which he had not means to do.[[47]] Willingly would he have pressed on northwards, but Fairfax was threatening Oxford, and the civilians, always anxious to keep the army in the south, clamoured loudly of the danger of the Duke of York, the Council, the Stores, and all the fair ladies of the Court. The said ladies also "earnestly by letter, solicited Prince Rupert to their rescue."[[48]] Reluctantly he faced southwards. But the danger of Oxford was less imminent than had been represented; Fairfax retired from before it. Then the contest of Rupert against Digby, the soldier against the civilian was renewed. "There was a plot to send the King to Oxford, but it is undone," the Prince wrote to his "dear Will." "The chief of the counsel was the fear that some men had that the soldiers would take from them the influence they now possess with the King."[[49]]

It was in accordance with the perversity of Charles's fate that just when the Parliamentary army had thrown off civilian shackles, he was ceasing to be ruled by the military counsels of his nephew. Rupert again urged a march to the North. Digby and the Councillors of Oxford, ever eager to keep the army in the South, recommended an attack on the Eastern counties. The King remained at Daventry hesitating between the two counsels, and in the meantime Fairfax and Cromwell were advancing towards him. Rupert's unaccountable contempt for the New Model Army prevented him from taking the proper precautions, and he remained absolutely ignorant of Fairfax's movements, until he was quartered eight miles from Daventry. Then the King decided to move towards Warwick, and that night he slept at Lubenham, Rupert at Harborough. On the same evening Ireton surprised and captured a party of Rupert's men, as they were playing at quoits in Naseby. A few who escaped, fled to warn the King, and the King hastened to Rupert. With unwonted prudence, Rupert advised retreat; reinforcements might be found at Leicester and Newark, and there was yet a hope that Goring might march to their aid. He did not know, as Fairfax knew through an intercepted despatch, that Goring was unable to leave the West. But Digby and Ashburnham were for fighting, and once again the civilian triumphed. On June 14th took place the fatal battle of Naseby.

Very early the royal army was drawn up upon a long hill which runs two miles south of Harborough. Here Astley intended the battle to be fought, resolving to keep on the defensive. But the enemy did not appear, and Rupert, growing impatient, sent out his scout master to look for them, about eight o'clock in the morning. The man returned, after a perfunctory search, saying that Fairfax was not to be seen. Then Rupert, unable to bear inaction any longer, rode out to look for him in person, with a small party of horse. At Naseby he found the whole army of the Parliament. It was just then engaged in shifting its position, and Rupert jumped to the conclusion that it was in full retreat. Lured on by this idea, he established himself on a piece of rising ground to the right, and summoned the rest of the army from its well-chosen position to join him there. This was perhaps the chief cause of the defeat that followed. Rupert and Maurice charged together on the right, and swept the field before them, till they reached the enemy's cannon and baggage waggons. Here Rupert was mistaken for Fairfax, for both were wearing red cloaks, and some of the Puritan reserve rode up, asking, "How goes the day?" The Prince responded by an offer of quarter, which was met by a volley of musket shot. But Rupert could not stay to complete his conquest. His part of the battle had been won, but behind him Cromwell had scattered the Royalist left, and was trampling the infantry of the centre in "a dismal carnage."[[50]] The King was turned from the battle too soon, his whole army was disheartened and overwhelmed, and Rupert returned too late, to find Cromwell in possession of the field. The Royal army was destroyed, and the war almost at an end. That night the King retreated to Ashby, and the next day, Sunday, he reached Lichfield, whence he hastened on to Raglan Castle. Rupert went on westward to the Prince of Wales at Barnstaple.