In 1644, Lilburne, having reached the rank of captain, returned to the north where he raised his own regiment of horse, which became part of Lord Fairfax's Northern Association army.

At the end of 1645, Ralph Weldon, colonel of the New Model Army's 8th Regiment of Foot, resigned to become governor of Plymouth, and Robert Lilburne was promoted to take his place early in 1646.

The majority in Parliament thereupon began to plan the reduction of the Army as surplus to requirements, some of the most troublesome regiments to be sent to Ireland, without addressing their arrears of pay.

[11] The soldiers addressed a petition to General Fairfax, supported by some of the most radical officers, among whom was Robert Lilburne, who was called before the House on 29 March to defend his action.

[12][13] At the same time, most of the officers in his regiment, who had formerly served under Colonel Weldon, petitioned Parliament to replace Lilburne with their lieutenant-colonel, Nicholas Kempson, and volunteered for service in Ireland.

[14][15] At some point during the ensuing revolutionary action, General Fairfax removed Liburne from the field by appointing him governor of distant Newcastle-upon-Tyne.

Cromwell had eight or nine of Lilburne's troopers arrested, and three ringleaders were sentenced to death, with one, private Richard Arnold, shot on the spot before the rest.

[11][18][19] The dispute between Parliament and the Army was interrupted by Charles I, who on 26 December 1647 signed an engagement with the Scots under the Duke of Hamilton to establish Presbyterianism in England in exchange for military assistance in regaining his throne.

[20] Conflict between England and Scotland had been active since 1639, largely over religious issues, when Charles I, king of both countries, attempted to force the episcopal Anglican church on the Presbyterian Scots.

The Scots responded by defeating England twice in the ensuing Bishops Wars, abolishing the episcopacy, and establishing a Presbyterian National Covenant.

[23] Presbyterian leaders in Scotland increasingly felt threatened by the radicalism of the Independents and some were willing to help restore King Charles, as the lesser evil.

[24] Beginning in May, Royalist uprisings in support of the king occurred in several places in England, notably in Kent and Colchester, which the Army under Fairfax put down.

[5] On 28 April 1648, Royalist forces under Marmaduke Langdale attacked Berwick-upon-Tweed and Carlisle in Northumberland, and took Pontefract Castle in Yorkshire, in order to establish a bridgehead for an invading Scots army.

According to Reid,[28] Hamilton had expected only to act as support for the Royalist uprisings, which by the time he reached England had already been put down, so that with the exception of Langdale, he was left to face the Army largely alone.

At the time of the invasion, Cromwell had been in Wales besieging the Royalist forces holding Pembroke Castle, and following its capitulation on 1 July, he immediately marched north with such speed that he left his artillery train behind.

[29] Lambert's cavalry delayed the invaders while Cromwell was en route, so that Hamilton reached Hornby Castle, Lancashire only by 9 August, when he turned west toward Preston and the bridge over the River Ribble.

On the morning of 17 August, with Hamilton's forces half-way across the bridge - most of the cavalry across, most of the infantry still on the north side - Lambert's vanguard began the attack on Langdale's position in the moors north-east of Preston.

His youngest brother Lt.-Colonel Henry Lilburne,[5] who had served under him in several of his commands since 1644, had recently been named Deputy Governor of Tynemouth Castle, when on 9 August he switched sides to support the king.

He sent his cavalry to Musselburgh, where Colonel Lilburne drove off a Scots attack on 31 July,[38] but Cromwell was forced to fall back on Dunbar where his navy could support him.

But the Scots assumed that he meant to evacuate by sea and were unprepared when, at dawn of 3 September, Lambert executed a surprise cavalry charge led by the regiments of Lilburne, Francis Hacker and Philip Twisleton, which claimed 3000 of the enemy killed and 10,000 taken prisoner.

[39][40] In August 1651 Charles II invaded England with a Scots army, and Cromwell shadowed his progress, leaving Colonel Lilburne in Lancashire with two regiments to block any Royalist reinforcements from joining the king.

[41] This was his most notable military action, praised even by the Royalist biographer Noble:[42] He attacked the loyal and truly great Earl of Derby in 1651 with three regiments, and defeated his lordship at Wiggan in Lancashire; and so completely, that of one thousand five hundred men that he (Derby) brought into the field, he hardly had thirty, when he escaped to King Charles II at Worcester; the engagement lasted about an hour.His report to Cromwell on the battle:[43] Wigan, 15th August, 1651.

[45] For the duration of Oliver Cromwell's tenure as head of state, as it devolved from a republican commonwealth to a military dictatorship, Lilburne maintained his loyalty.

During the Rule of the Major-Generals he was appointed on 19 October 1655 (retaining the rank of colonel) as deputy to John Lambert, responsible for the day-to-day administration of Yorkshire and County Durham.