With the arrival of Prince Rupert, the Parliamentarian forces led by generals Leven, Fairfax and Manchester abandoned the siege of York and headed south. Rupert followed and attacked the rear of the column forcing the fleeing army to stop. The Parliamentarians held the higher and tactically better position on Long Marston Moor. The Duke of Newcastle and his Royalist men joined Prince Rupert to create an army of around 18,000 men while the Parliamentarians had a force of around 28,000 men and had better artillery. Late in the day the fighting began with an attack by Leven and Fairfax in the centre. The attack did not go well for the Parliamentarians and Leven and Fairfax left the battlefield. Whan all seemed lost a cavalry unit commanded by Oliver Cromwell on the left of the field attacked the Royalists and gained the upper hand. The Royalists were defeated leaving some three to four thousand of their men dead.

The Self-Denying Ordinance was passed by the Lords after extra clarification was provided. The Ordinance set the size of the army to around 22,000 men and suggested the army should be controlled by Sir Thomas Fairfax.

Sir Thomas Fairfax and the New Model Army caught the King at Naseby Field in Northamptonshire. Cromwell joined Fairfax and the combined Parliamentary force consisted of some 14,000 men while the King and Prince Rupert had around half that number. The King had a better position on the battlefield and had more experienced soldiers while some of the Parliamentary men were raw conscripts. For the Parliamentarians, Skippon commanded the infantry, Cromwell commanded the Ironsides to the left and to the right Ireton commanded his men. Both Skippon and Ireton were injured in the battle. Ireton was captured but managed to escape. Cromwell's Ironsides routed the Royalist army and the battle was won. King Charles was defeated. King Charles and his cavalry escaped to Leicester but he left has baggage train behind unprotected. Large amounts of the King's and his supporters money was captured by the Parliamentarians along with the King's personal letters.

The Royalist defeat was complete when the King's men at Leicester surrendered to Fairfax and handed over their weapons and horses.

Fairfax went to the south west to deal with the Royalist Lord Goring and the western army. The two armies met at Langport in Somerset. Goring set a trap for Fairfax in the narrow lanes of the countryside with musketeers hidden in the hedges lining the lanes. He also had two cannons positioned to fire down the lane on the attackers. This did not stop the powerful New Model Army whose own guns silenced the Royalist cannons. The Royalist cavalry were forced back leaving the musketeers exposed and picked off by their Parliamentary opposites. The royalists set fire to Langport and began retreating to Bridgwater with the Parliamentarians in pursuit, led by Cromwell and his Ironsides.

Fairfax besieged Bridgwater in Somerset. The siege didn't last long as Fairfax had the fortifications scaled by ladders and the town surrendered.

The Parliamentarians captured the city of Bath.

After a two week siege the castle at Sherborne fell to the Parliamentarians.

Fairfax surrounded the city of Bristol which was held by Prince Rupert and several thousand Royalists soldiers. After a short siege Fairfax ordered an early morning assault on the city. Bristol fell to the Parliamentarians.

Only days after Hopton had taken charge of the Royalist forces in the south-west, Fairfax attacked and took the castle at Dartmouth capturing many guns and many prisoners.

Fairfax caught up with Hopton who was in North Devon at Torrington. The attack by Fairfax drove Hopton from the town and captured many of his men. Hopton managed to escape into Cornwall with several thousand horsemen but his men were demoralised and had started to desert him.

On March 13/14 Hopton finally surrendered to Fairfax at Truro. Charles, the Prince of Wales, had escaped earlier, sailing first to the Scilly Isles and then to Jersey in the Channel Islands.

After accepting the surrender of Hopton, Fairfax turned to the city of Exeter which surrendered to him in early April.

The armies of Fairfax and Cromwell surrounded the city of Oxford where King Charles was besieged. Negotiations were held in an attempt to get a peaceful solution rather than lose men in a costly assault, but before the city surrendered Charles managed to escape in disguise. Charles hoped that the Scots would support his cause against Parliament. Charles had been using the French envoy, Jean de Montreuil, to communicate with the Scots.