Sometimes severely defeated, more often successful, and always energetic, prudent and resourceful, they contrived to keep up the struggle until the crisis of 1644, when York was held by the Marquess of Newcastle against the combined forces of the English Parliamentarians and the Scots, and Prince Rupert hastened with all available forces to its relief. A gathering of eager national forces within a few square miles of ground naturally led to a battle, and Marston Moor (2 July 1644) proved decisive for the struggle in the north. The younger Fairfax bore himself with the greatest gallantry in the battle, and though severely wounded managed to join Oliver Cromwell and the victorious cavalry on the other wing. One of his brothers, Colonel Charles Fairfax, was killed in the action. But the Marquess of Newcastle fled the kingdom, and the Royalists abandoned all hope of retrieving their affairs. The city of York was taken, and nearly the whole north submitted to the Parliament.

In the south and west of England, however, the Royalist cause was still strong. The war had lasted two years, and the nation began to complain of the contributions that were exacted, and the excesses that were committed by the military. Dissatisfaction was expressed with the military commanders, and, as a preliminary step to reform, the Self - denying Ordinance was passed. This involved the removal of the Earl of Essex from the supreme command, along with other Members of Parliament. This was followed by the New Model Ordinance, which replaced the locally raised Parliamentary regiments with a unified army. Sir Thomas Fairfax was selected as the new lord general with Cromwell as his lieutenant - general and cavalry commander. After a short preliminary campaign the "New Model" justified its existence, and "the rebels' new brutish general", as the king called him, proved his capacity as commander - in - chief in the decisive victory of Naseby (14 June 1645). The king fled to Wales. Fairfax besieged Leicester, and was successful at Taunton, Bridgwater and Bristol. The whole west was soon reduced.

Fairfax arrived in London on 12 November 1645. In his progress towards the capital he was accompanied by applauding crowds. Complimentary speeches and thanks were presented to him by both houses of parliament, along with a jewel of great value set with diamonds, and a sum of money. The king had returned from Wales and established himself at Oxford, where there was a strong garrison, but, ever vacillating, he withdrew secretly, and proceeded to Newark to throw himself into the arms of the Scots. Oxford capitulated following the final siege of Oxford, and by the end of September 1646 Charles had neither army nor garrison in England, following the surrender of Thomas Blagge at Wallingford Castle after a siege conducted by Fairfax. In January 1647 he was delivered up by the Scots to the commissioners of parliament. Fairfax met the king beyond Nottingham, and accompanied him during the journey to Holdenby, treating him with the utmost consideration in every way. "The general", said Charles, "is a man of honour, and keeps his word which he had pledged to me."

With the collapse of the Royalist cause came a confused period of negotiations between the Parliament and the king, between the king and the Scots, and between the Presbyterians and the Independents in and out of Parliament. In these negotiations the New Model Army soon began to take a most active part. The lord general was placed in the unpleasant position of intermediary between his own officers and Parliament. To the grievances, usual in armies of that time, concerning arrears of pay and indemnity for acts committed on duty, there was quickly added the political propaganda of the Independents, and in July the person of the king was seized by Cornet Joyce, a subaltern of cavalry — an act which sufficiently demonstrated the hopelessness of controlling the army by its articles of war. It had, in fact, become the most formidable political party in the realm, and pressed straight on to the overthrow of Parliament and the punishment of Charles.

Fairfax was more at home in the field than at the head of a political committee, and, finding events too strong for him, he sought to resign his commission as commander - in - chief. He was, however, persuaded to retain it. He thus remained the titular chief of the army party, and with the greater part of its objects he was in complete, sometimes most active, sympathy. Shortly before the outbreak of the Second Civil War, Fairfax succeeded his father in the barony and in the office of governor of Hull. In the field against the English Royalists in 1648 he displayed his former energy and skill, and his operations culminated in the successful siege of Colchester, after the surrender of which place he approved the execution of the Royalist leaders Sir Charles Lucas and Sir George Lisle, holding that these officers had broken their parole. At the same time Cromwell's great victory of Preston crushed the Scots, and the Independents became practically all-powerful.

John Milton, in a sonnet written during the siege of Colchester, called upon the lord general to settle the kingdom, but the crisis was now at hand. Fairfax was in agreement with Cromwell and the army leaders in demanding the punishment of Charles, and he was still the effective head of the army. He approved, if he did not take an active part in, Pride's Purge (6 December 1648), but on the last and gravest of the questions at issue he set himself in deliberate and open opposition to the policy of the officers. He was placed at the head of the judges who were to try the king, and attended the preliminary sitting of the court. Then, convinced at last that the king's death was intended, he refused to act. In calling over the court, when the crier pronounced the name of Fairfax, a lady in the gallery called out that the Lord Fairfax was not there in person, that he would never sit among them, and that they did him wrong to name him as a commissioner. This was Lady Fairfax, who could not forbear, as Bulstrode Whitelocke says, to exclaim aloud against the proceedings of the High Court of Justice.

His last service as commander - in - chief was the suppression of the Leveller mutiny at Burford in May 1649. He had given his adhesion to the new order of things, and had been reappointed lord general. But he merely administered the affairs of the army; when in 1650 the Scots declared for Charles II, and the council of state resolved to send an army to Scotland in order to prevent an invasion of England, Fairfax resigned his commission. Cromwell desired to see him continue as commander - in - chief, as did those planning the war, but Fairfax could not support the war. Cromwell was appointed his successor, "captain - general and commander - in - chief of all the forces raised or to be raised at authority of Parliament within the Commonwealth of England."

Fairfax received a pension of £5000 a year, and lived in retirement at his Yorkshire home of Nunappleton until after the death of the Lord Protector in 1658. Nunappleton and Fairfax's retirement there are the subject of Andrew Marvell's country house poem, 'Upon Appleton House'. The troubles of the later Commonwealth recalled Lord Fairfax to political activity, and for the last time his appearance in arms helped to shape the future of the country, when George Monck invited him to assist in the operations about to be undertaken against John Lambert's army. In December 1659 he appeared at the head of a body of Yorkshire gentlemen, and such was the influence of Fairfax's name and reputation that 1,200 horse quit Lambert's colours and joined him. This was speedily followed by the breaking up of all Lambert's forces, and that day secured the restoration of the monarchy. In the subsequent elections, Fairfax was elected member of Parliament for Yorkshire, and was put at the head of the commission appointed by the House of Commons to wait upon Charles II, at the Hague and urge his speedy return. Fairfax provided the horse on which Charles rode at his coronation.

Fairfax had a taste for literature. He translated some of the Psalms, and wrote poems on solitude, the Christian warfare, the shortness of life, etc. During the last year or two of his life he wrote two Memorials which have been published – one on the northern actions in which he was engaged in 1642 - 1644, and the other on some events in his tenure of the chief command. At York and at Oxford he endeavoured to save the libraries from pillage, and he enriched the Bodleian with some valuable manuscripts. His correspondence, were edited by GW Johnson, and were published in 1848 - 1849 in four volumes.

The metaphysical poet Andrew Marvell authored "Upon Appleton House, To My Lord Fairfax", nominally about Fairfax's home, but also his character as well as England during his era.

The remaining eleven years of the life of Lord Fairfax were spent in retirement at his seat in Yorkshire. Fairfax died at Nunappleton, and was buried at Bilbrough, near York.

He married Hon. Anne de Vere, daughter of Horace Vere, 1st Baron Vere of Tilbury and Mary Tracy, on 20 June 1637. They had a daughter, Hon. Mary Fairfax (b. 30 Jul 1638 - d. 20 Oct 1704). who married George Villiers, 2nd Duke of Buckingham. Sir Thomas was succeeded as Lord Fairfax by a cousin, Henry Fairfax, 4th Lord Fairfax of Cameron.

As a soldier he was exact and methodical in planning, in the heat of battle "so highly transported that scarce any one durst speak a word to him" (Whitelocke), chivalrous and punctilious in his dealings with his own men and the enemy. Honour and conscientiousness were equally the characteristics of his private and public character. But his modesty and distrust of his powers made him less effectual as a statesman than as a soldier, and above all he is placed at a disadvantage by being both in war and peace overshadowed by his associate Cromwell.