The way was shortly open for a forward movement by the Roundheads, and it soon began. The campaign that ended in the battle of Marston Moor began like a game of chess. For months the Roundheads in Lancashire, helped by Fairfax, had overpowered the Royalists everywhere except at Lathom House (near Ormskirk), defended by the Countess of Derby. Rupert had to wait until May before he could leave the Midlands for its relief, and by that time other troubles had arisen. The Royalists were shut up in York and besieged by the Roundheads.

Rupert now determined on a bold stroke, which relieved Lathom House and left him free to proceed to York. This city was reached on July 1st. The Royalist Marquis of Newcastle could now escape, and the two royal armies at once took up their quarters at Marston, six or seven miles west of York; the Scots and Fairfax, now joined by the Earl of Manchester and Cromwell, drawing off a little to the south.

It looked as if Rupert's movement had been a complete success, But he was not content with relieving the Northern army; he wished to inflict a decisive defeat on the Parliamentarians. He told the more cautious Newcastle that he had the king's most positive orders to fight at all costs. But the king was ignorant of the circumstances. Newcastle, Rupert, and Goring had not more than eighteen thousand men, whilst Manchester and Cromwell, the Fairfaxes and the Leslies mustered about twenty-seven thousand. Rupert, however, had his way. He seized a strong position with open ground in front, where his cavalry could move easily.

The Parliamentary army had also a good position on a slope or ridge between Tockwith and Long Marston. A ditch and hedge hindered their attack, and neither side wished to risk being caught there. For hours on the afternoon of July 2nd the armies lay facing one another. They were in the usual sort of order, foot-soldiers in the middle and cavalry on each side. Manchester was in chief command. Cromwell and David Leslie, with 4,000 horsemen, were on the left; next them came Manchester's foot; next the Scottish foot under Alexander Leslie; next Lord Fairfax's foot; and on the right wing Sir Thomas Fairfax's Yorkshire cavalry.

Opposite them Rupert's own cavalry faced Cromwell's; Newcastle's foot faced the middle, and Goring's cavalry faced Fairfax. Cromwell was only in subordinate command, but as events turned out it was his  battle. "Is Cromwell there?" asked Rupert of a prisoner. "And will they fight? If they will, they shall have fighting enough." "If it please God," said Cromwell, "so shall he."

At six o'clock no movement had been made. "We will charge them to-morrow morning," said Rupert, and went off to supper. In a few minutes Cromwell had begun the attack. Sending a body of dragoons to clear the way over the ditch and hedge, he followed up rapidly with some heavy cavalry. A regiment of Rupert's horse met them and were swept back. This brought, Rupert himself to the front, rallying his men. And now the stoutest and fiercest troopers on both sides charged with all their force.

"We came down the hill in the bravest order and with the greatest resolution that ever was seen," wrote one of them afterwards. "Cromwell's division of 300, in which himself was in person, charged the first division of Prince Rupert's, in which himself was in person. Cromwell's own division had a hard pull of it. They stood at the sword's point a pretty while, hacking one another, but at the last, so it pleased God, he brake through them, scattering them before him like a little dust."

David Leslie, with another body of cavalry, was now supporting Cromwell, and together they routed Rupert's horsemen completely, although Cromwell was wounded on the neck and for a time disabled.

This, however, was only part of the battle. Further along the line Manchester's foot, led by Crawford, had made a successful attack, but in the centre, the Scottish foot, led by Alexander Leslie (Lord Leven) and William Baillie, were hard pressed by Newcastle's Whitecoats, and so also were Lord Fairfax's foot; whilst on the extreme right, Sir Thomas Fairfax's cavalry were being swept off the field by Goring's horse. The bulk of Goring's men pursued Fairfax's retreating regiments for miles. On that side the Royalists believed themselves sure of victory, and already sent off messengers to Oxford to announce it; and no wonder, for many had fled as far as Tadcaster, and old Leven reached Wetherby thinking the battle was entirely lost. Meanwhile Fairfax, wounded and almost alone, managed to reach Cromwell to tell him the news of the disaster.

By this time the left wing, Cromwell's and Leslie's cavalry, were occupying the ground from which they had swept Rupert. They could thus wheel round still further and close in upon the Royalist infantry—Newcastle's—who were in a deadly struggle against Crawford and a few Scottish regiments. Crawford's foot had from the first pressed back the enemy, and with the Scottish regiments who kept their ground, he saved the situation, until Cromwell and Leslie with the victorious cavalry could come to their help.

The decisive movement was Cromwell's. First clearing the ground of the few undefeated horsemen who had not joined in the pursuit of Fairfax, he and Leslie now bore down on the mass of Newcastle's foot, and caught them between his own horsemen and Crawford and Baillie's foot. The slaughter was terrible. Newcastle's finest regiments made a gallant and desperate stand. "By mere valour, for one whole hour, they kept the troops of horse from entering amongst them at near push of pike; and when the horse did enter, they would have no quarter, but fought it out until there was not thirty of them living."

By nine o'clock all was over. Four thousand Royalists had been killed. Newcastle rode off to Scarborough and took ship to the Continent. Rupert collected the remnants of his army, 6,000 men, left York to the Roundheads, and rode off towards Chester. It was the first great and decisive victory of the Parliamentary armies, and whilst many had fought bravely, the victory was chiefly due to Cromwell's judgment and resolution and to the irresistible onslaught of his Ironsides. It was in this battle that Rupert gave Cromwell the nickname "Old Ironside," and his own soldiers accepted it. "We never charged but we routed the enemy. God made them as stubble to our swords"; so wrote Cromwell in describing the battle.

After Marston Moor, Cromwell persuaded Parliament to reorganise the army, and a fine "New Model Army" was the result; the half-hearted leaders were also got rid of.

Soon the two armies again met in the decisive battle of Naseby. Charles, with Rupert and Langdale and Astley—for Goring was unable to join in time—had only 9,000 men. Fairfax had 14,000. But the king had heard of the new army, and thought his own old soldiers would make short work of it. He despised Fairfax, the new "brutish general," as he called him. And, indeed, but for Cromwell's unerring judgment and resolution, the king's confidence might have been justified. It was, compared with some others, a simple battle.

On the Parliamentary side, Skippon was in the middle with the infantry. Ireton had some cavalry on the left. Cromwell, with over 3,000 horse, had the right wing. On the opposite side Rupert faced Ireton, Astley faced Skippon, and Sir Marmaduke Langdale faced Cromwell.

Rupert swept all before him, and Ireton, with five regiments, was driven back. Ireton himself was wounded, and was for a time a prisoner. But, as usual, Rupert went too far. Whilst he was capturing the baggage train, the main action was being neglected. Astley's foot held the centre in check, and on the side where Rupert's horse had swept off Ireton, the Roundheads were exposed to a flank attack. Skippon himself was severely wounded.

It was Cromwell who, by the same tactics as he had used at Marston, once more turned the scale. He sent forward Whalley, with a regiment of Ironsides, to charge Langdale. They carried all before them, and this left Cromwell, with his reserve cavalry, free to charge the Royalist centre. Joined by Fairfax, he soon made an end of the king's foot regiments. Before Rupert could return, whole regiments had surrendered, and the rest were flying back towards Leicester. A thousand had been killed. Five thousand prisoners, the king's baggage, his artillery, and his letters, fell into the Parliament's hands.

From Naseby to the end of the first civil war, the time was spent in crushing out isolated fragments of the Royalist army, and in capturing fortified houses and castles. Goring was finally crushed at Langport, in Somerset, while Bristol, defended by Rupert, capitulated early in September. Bridgwater, Lyme, Taunton, Bath, Winchester, Devizes, Sherborne, all fell in a few weeks.

Long and tedious were the attempts that Charles made to get terms from the Parliament, and meanwhile he kept up the game of trying to secure support, now from the Irish, now from the Scots. At length, at three in the morning of April 27th, 1646, disguised as a servant, with his beard and hair closely trimmed, Charles rode out of Oxford, over Magdalen Bridge, and by a roundabout route, passing through Slough, Harrow, St. Albans, Melton Mowbray, and Stamford, reached Southwell on May 7th at seven in the morning. The distinguished personage who was supposed to be his master pretended to be on the Parliament's side, and thus got through the Roundhead patrols with little difficulty. In a few hours Charles had surrendered himself a prisoner to the Scottish army encamped at Newark. The Scots had now a great prize in their hands, and moved off to Newcastle,

Charles was a prisoner with the Scottish army from May to December, 1646. Long. discussions went on, and the Presbyterians tried to convert the king to their form of religion. But Charles refused to come to terms, as they asked him to give up the English Church and establish Presbyterianism, at least for ten years. The English Parliament, also largely Presbyterian, bargained with the king and with the Scots. It was arranged that the Scots should hand over the king to the English Parliament, on receiving payment of their arrears. In January, 1647, therefore, Charles was lodged under guard at Holmby House, in Northamptonshire, and the Scots went home.

And now there began a most extraordinary series of bargainings between king, Parliament, and army. The two latter quarrelled; Cromwell threw in his lot with the army and had Charles seized and brought to the army headquarters at Newmarket.

The army was now supreme, and made Charles an offer called the Heads of the Proposals. The king was to be restored, but for ten years Parliament was to control the militia, and the appointment of ministers of the Crown. These terms were refused. The quarrels between the different parties continued, Charles escaped to the Isle of Wight, and early in 1648 the second civil war broke out, after Charles had managed a treaty with the Scots.

The Royalists were besieged at Colchester, and Cromwell gained a decisive victory over the Scots at Preston, and the second civil war (April–August, 1648) was soon over.

After this there was little hope of mercy for the king. The army had made up its mind that Charles was responsible for all the blood shed during the second civil war. The Presbyterians still wished to treat with the king, but the army officers on December 6th sent Colonel Pride to Westminster to turn out the Presbyterians by force. Standing with a guard of soldiers at the entrance to the Parliament House, he arrested forty-five members, turned back ninety-six others, and admitted only those, about fifty or sixty, who were known to be in agreement with the wishes of the army. This action of Colonel Pride is known as "Pride's Purge."