The defeat of Rupert at Marston Moor completely destroyed the King's chances of victory in the Civil War, but less than two months later his triumph over Essex at Lostwithiel, where all the Parliamentarian foot were obliged to surrender, gave his cause a new lease of life in the south of England. The winter was passed in fruitless negotiations; when they had broken down the New Model Ordinance was passed through Parliament, and in the spring of 1645 the toils began to close round the King who left Oxford and marched northwards with Rupert.

Thus once more Lancashire was brought into the general course of events. It was feared that Charles would try to break through to join the Earl of Montrose in Scotland; instead of advancing Leven retreated, notwithstanding remonstrances from Sir Thomas Fairfax. The Fairfaxes themselves were at York, and thus Lancashire was left completely undefended. The leaders were in great consternation. Already in the middle of March, 1645, it was feared that the King would march on Shropshire and Cheshire, and the Committee of Both Kingdoms wrote to Sir George Booth to be careful to guard Warrington.[166] Two months later the danger was acute; if the King could enter Lancashire he might indefinitely increase his forces. Charles penetrated into Cheshire in May, and obliged Sir William Brereton to raise the siege of Chester and draw his men into garrisons. Fairfax promised to send 1,500 men in order to hinder the King's advance, and the Lancashire leaders were urged to keep careful watch over all the passes into that county, and to have 200 horse and 1,000 foot ready to send to any rendezvous which Fairfax and Leven might appoint. Colonel Assheton's regiment was recalled in haste from Cheshire. The ford at Hale was guarded by 1,100 foot and 4 troops of horse, and the general rendezvous was appointed at Barlow Moor, near Manchester, on Thursday, May 19th. The Lancashire troops, however, attended in small numbers. They were greatly disorganised and the county much wasted by three years of war; and they complained of the place chosen for the rendezvous as being too near to plague-stricken Manchester. Lathom was still a thorn in the side of the Parliamentarians of the county, and they were obliged to leave some troops at Ormskirk to continue the siege; there remained only one company of foot to defend both Liverpool and Warrington, and one of Egerton's regiments flatly refused his order to march. On May 22nd the Lancashire Committee wrote to London that they had obeyed the orders regarding the disposition of troops, "but it is more difficult to defend the country near Manchester, the river being shallow, and the Scots and Cromwell both marching further off than was expected." Next day Sir William Brereton wrote from Manchester, giving a very gloomy picture of affairs. "The forces assigned for the passes are inconsiderable, the passes many and indefensible." All the men he could spare were on the borders of Cheshire but they were quite inadequate to oppose the King if he should try to enter Lancashire. A few days before the Earl of Callander had sent a letter to the Scotch Commissioners in London to the same effect. "If we should abandon Yorkshire to go into Lancashire, this county would lie open to the King, and York will probably be lost; if we stay here the King is at liberty to enter Lancashire and increase his army, because of the many disaffected persons in that county. It is impossible to defend both places which is a line of 80 miles, at once, the ways and passages also between those counties being such as the forces in one county cannot without very great difficulty and marching a long way give assistance to the other."[167]

All this may have been exaggerated, but there is no doubt that Lancashire was in a state of great distress. Fortunately for the Parliamentarian party, however, the King's position was even worse than their own. Weak as they were, he was in no condition to force an entrance into hostile territory. The resistance offered may have been inadequate, but the appearance of force was enough to turn him in another direction. On May 21st he was at Whitchurch, 'not 24 miles from Hale Ford'; but he came no nearer to Lancashire than Market Drayton, but turned eastwards into the Midlands, and on May 31st took Leicester by storm.[168]

There were further fears of Charles in September when he was in Cheshire; but his defeat at Rowton Heath disposed of that danger. Even in October when he was at Welbeck, it was feared that his plan was to march northwards to relieve Skipton and Lathom, and to recruit his foot in Lancashire, "where Manchester will be as easily entered as attempted"; but the defeat of Langdale, near Pontefract, removed this danger too.[169]

Meanwhile the siege at Lathom House dragged on. During the winter of 1644 the garrison was practically unmolested, so that they were able to make little plundering expeditions, riding out after nightfall and returning to the house before daylight. Sometimes they even ventured further afield into the Fylde country. So great was the nuisance occasioned by their plundering and that of the royalists at Greenhalgh, that in December a local "cessation" was effected; but the Parliament promptly annulled it. At length the Committee at Manchester decided to re-form the siege, and Colonel Egerton was chosen for command. (January, 1644‑5.) Troops were provided out of all the county, but no serious attempt was made to storm, the object being rather to starve out the garrison. In the House were a numerous garrison under Colonel Rawsthorne and Colonel Vere, who had with them Charnock, Key, Molyneux Radcliffe, Farington and other Captains who had taken part in the first siege. There seem to have been three divisions of the royalists, the main guard being in Lathom itself, and others at New Park; while the third division consisting of the Irish troops who had been at Liverpool during the previous summer occupied the Lodge.

The Parliamentarian engineer was Colonel Morgan, who had also taken part in the first siege. No trenches were made close to the house, but under his direction a deep ditch was drawn round the wall at some distance, and the attacking force lay on the outer side of that. There would only be fighting when the garrison sallied out for stores. The siege made very slow progress. On March 25, 1645, Egerton writes very despondently to the Speaker concerning the state of the siege and the discipline of his troops. It was now nearly three months since he had first advanced, and in spite of promises his force was so small that he dared not approach nearer than four or five miles from the House. Most of the troops had been got together by his own efforts. He had at first advanced to within two miles, but finding that he could not stop the garrison plundering, he had retired again and spread out his men, who only numbered 100 foot and 400 horse. Even these were constantly deserting, and trying to take their colours with them.[170] Some months before this Meldrum had written that the Colonels of three regiments "told me plainly that if I should press the soldiers to an approach which would require them to lie in the trenches without shelter, where there was neither money nor victuals, they would all be gone do what we could to prevent it."[171]

By the middle of July, however, the Parliamentarian troops had made a considerable advance, for they carried the Lodge by storm, forty of the defenders being killed and sixty taken prisoners; and soon afterwards the garrison at New Park also surrendered, after which the royalists were confined to Lathom itself. In August, two of the Earl of Derby's servants named Sharples and Moreau, came over from the Isle of Man, and were captured in trying to get through the besiegers' lines. Sharples was sent into the House that he might explain the hopelessness of resistance, but in vain. The garrison refused to be convinced, and Sharples was allowed to return to the Earl of Derby. For three months more the royalists held out. But it was an unnecessary display of courage, and was bound to have disastrous results for Lathom House. This second siege was very different from the first. The glamour of Lady Derby's presence was gone. Instead of a numerous garrison well armed and provisioned, making successful sorties at intervals, and hopeful of release from without, there were only a few irreconcilables being gradually starved into submission. And they had nothing to gain by prolonging the war, for after the Battle of Naseby the royalist cause was dead.

After the defeat of Charles at Rowton Heath in September, 1645, he sent word to Lathom that there was no longer any prospect of relief from him, and the garrison had better therefore surrender. It would appear, however, that negotiations had already been entered into. Very favourable terms were at first offered. The House with all its contents were of course to be surrendered; but the garrison might freely depart, and Lady Derby and her children were to be allowed to live at Knowsley House with one-third of the Earl's estate for their support. Seacome states that these terms were freely offered by Egerton, and were only broken off by the obstinacy of one of the royalist Commissioners, who absolutely refused to agree unless the cannon were allowed to remain at Lathom for its defence. Actually, however, it would seem that the Committee of Both Kingdoms interfered, and forbade the conclusion of the negotiations. If suitable terms should be proposed, they professed to be willing to consider them.[172]

By the middle of November the shortage of provisions of the garrison had become so great that another parley was requested. A place was appointed, and the two sides again met; but even now they could not agree, the royalists refusing to accept any terms except those which they themselves proposed. The conference was broken off and they returned outwardly confident to Lathom; but their action was really just as much a piece of bluff as Rigby's last demand for surrender during the first siege in May, 1644. The tables were now turned, and it was Rigby's shrewdness which perceived how desperate the condition of the garrison was. When they were gone, Colonel Alexander Rigby said to the rest of the Colonels and Commanders then present that "he was persuaded that notwithstanding their seeming stoutness and highness of stomacke they could not hold out long, the smell and taste of their garments bewraied it."[173] Nevertheless the garrison did hold out for three weeks longer, and it was the beginning of December before the great House was at last starved into surrender. The final agreement was made between Colonel Booth on one side, and Colonel Nowell, Colonel Vere, and two others on behalf of the royalists. The terms were as follows:—The House with all its plate and furniture, and all the horses and arms of the garrison were to be delivered up to the Parliament; only the Governor might take his horse and pistols and £10 in money. Officers above the rank of Lieutenant were allowed their swords, but all below that rank and all the common soldiers were to depart unarmed. Convoy was to be provided for them to Aberconway, which was the nearest royalist garrison not besieged.[174]