In Lancashire the way was now open for the siege of the last royalist strongholds. Only two places still held out to the King, Lathom House and Greenhalgh Castle, and of these the former was much the more important.

The Earl of Derby was still in the Isle of Man, but Lathom under the able direction of the Countess of Derby, assisted by such Lancashire royalists as still remained in the county, had been gradually prepared for resistance. It being almost the only place of refuge left, many of the militant royalists had gathered there. The House had been summoned as far back as May, 1643, after the capture of Warrington; but nothing had been done towards reducing it. The royalists had been, however, practically confined to the Park at Lathom, and Rigby sent what troops he could spare to harass them at intervals. The garrison on their part plundered all they could. Early in February, 1644, the royalists had the better of a skirmish with some Parliamentarian horse under Captain Hindley; and when the danger in Cheshire was over the troops from Cheshire were at liberty to begin the reduction of Lathom.

The first siege of Lathom House is quite the most picturesque incident of the Lancashire war. More has been written about it, and it is probably better known than any other event. This has rather served to disguise the fact that the siege was not very important from a military point of view. There was no great issue depending upon its capture as in the case of that of Manchester in October, 1642, or of Warrington in April, 1643; its resistance for a few months more or less did not affect the general position. It was a centre of hostile influence, but its garrison was bound to be only on the defensive and could never hope to be strong enough to make Lathom the starting point for a re-conquest of Lancashire for the King. Thus the defence was in the nature of a forlorn hope, and derived from this greater interest; when it is added that the defence was directed by a woman after the Earl of Derby and lesser royalist leaders had been driven out of the county, it easily became 'ever memorable' to the royalists. The attempt to save a splendid and historic mansion from the destruction which afterwards unhappily overtook it makes a further appeal to the imagination; and that the attempt was successful owing to the appearance on the scene of the chivalrous figure of Prince Rupert, supplies the last touch of sentimental interest.

Nothing now remains of old Lathom House and no picture of it is known to exist. Its situation and appearance was accurately described by Seacome, but it is impossible now even to identify the site.[124] Lathom House in those days was strong not only from its situation but from its structure. It stood upon marshy ground in a hollow surrounded by small hills which made it very difficult to effect an approach to the walls. The wall itself was six feet thick, and the whole was surrounded by a moat twenty-four feet across and six feet deep; a palisade between the walls and the water provided a further defence. On the wall were nine towers upon each of which were planted six guns, three turned one way and three the other, and in the centre of the building was a higher tower called the Eagle Tower. The gate house, which was a strong and lofty building, stood at the entrance to the first court.

On Saturday, February 24, 1644, it was decided at a meeting of the Committee at Manchester that Colonels Assheton, Rigby and Moore should undertake the siege of Lathom House.[125] News of this came to Lathom on Sunday, and the Countess of Derby at once sent out to obtain information from a friend which she had in the enemy's camp, while hastening on the reinforcement and provisioning of the garrison. The messenger returned on the following day with the news that the Parliamentarian troops had already marched as far as Bolton, Wigan and Standish. On Tuesday, February 27, they had taken up their quarters round the house at a distance of from one to three miles from it. The rest of the week was spent in negotiations. A formal summons of surrender was first brought on Wednesday by Captain Markland from Sir Thomas Fairfax, who further promised that he would use his influence with Parliament if the Earl of Derby would submit himself to their mercy. Lady Derby asked for a week's delay in which she might send a message to the Earl to know his opinion. This was refused, and Fairfax then requested her to come in her coach to New Park, a house about a quarter of a mile from Lathom, in order to have a personal interview with himself and his Colonels. But the Countess remembering her birth, returned a haughty refusal, "conceiving it more knightly that Sir Thomas Fairfax should wait upon her than she upon him." After two more days of messages Assheton and Rigby entered Lathom with propositions, which as might have been expected were severe. The House and all arms and ammunition were to be delivered up, the garrison having leave to depart to Chester or elsewhere; Lady Derby was to reside at Knowsley, being allowed 20 musketeers for her protection, or she was to join the Earl in the Isle of Man. These conditions were refused "as in part dishonourable in part uncertain." On Monday, March 4, Assheton came again alone in order to receive the royalist proposals. These required a month's delay for the removal of Lady Derby and her family to the Isle of Man, during which time the royalist garrison was to be kept at Lathom; but afterwards none of the arms were to be employed against the Parliament. After her departure none of the tenants of the Earl were to be molested. It was evident, however, that all negotiations were useless. On their own confession the royalists did not believe that Fairfax's promises were genuine, nor did they intend to keep their own. The Parliament referred to in their proposals was understood by them to mean the King's Parliament at Oxford. The only object of allowing negotiations at all was in order to gain time to put the House into a better state for defence. The besiegers, however, made one final offer which was brought by Colonel Morgan, the assistant engineer, "a little man short and peremptory";[126] they allowed the time which had been asked for to evacuate Lathom, but the cannon were to be left for its defence and not removed with the rest of the arms and goods. By 10 o'clock the following day all the royalist garrison was to be disbanded and 40 Parliament soldiers to be received as a guard. The royalists, however, seeing that there was now no more time to be gained, formally broke off all negotiations. The defiant answer was at length given which had been kept in the background for a week. The Countess of Derby refused all their articles, and declared "That though a woman and a stranger, divorced from her friends, and robbed of her estate, she was ready to receive their utmost violence trusting in God both for protection and deliverance."

Seacome states that at some point in the negotiations Sir Thomas Fairfax himself visited the House, and that Lady Derby drew up all her garrison in an imposing array, from the main guard in the first court to the great Hall where she herself received him. This ruse had its desired effect; so impressed was Fairfax with the strength of the garrison that he dissuaded the other leaders from making an immediate attack, which was just what the garrison most feared.[127] The besiegers now moved their lines nearer to the walls. But even now all treaty was not at an end. Nothing much was done during the rest of the week; but on Sunday, March 10, a deputation of tenants was persuaded to enter Lathom to plead with Lady Derby to surrender; but once inside the gates their royalism was apparent and the pleading was not very powerful. Yet once more, however, on the day following (Monday, March 11) Captain John Ashhurst, whom the royalists praise for his courtesy, came in with a last proposal from Fairfax. All former conditions were to be waived; the Countess, all the garrison and all the household were to have liberty to depart wherever they pleased with all their arms, ordnance and goods, yielding up the house to Sir Thomas Fairfax. The arms, however, were never to be employed against the Parliament; and everyone must leave the house at once excepting a hundred people who might remain ten days. This was of course refused, and all negotiations were now at an end.

The siege now began to be pressed with more vigour. The royalist garrison consisted of 300 men. Lady Derby was called Commander-in-Chief, with Mr. Farington as her chief adviser; and the Captains were Farmer, Ogle, Molyneux, Radcliffe, Chisenhale, Rawsthorne, Charnock, and Fox. Farmer, who was made Major of the House, was a Scotchman who had seen service in the Low countries. He was afterwards killed at Marston Moor. Rawsthorne, then Colonel, was in chief command during the second siege. The garrison was divided equally among all the Captains, who had therefore not quite half a company each. Half the garrison was on duty every night, and 16 marksmen from the whole number kept watch all day on the Towers.

The Parliamentarian soldiers before Lathom were drawn out of each Hundred by turns, their whole number being between 2,000 and 3,000. At first the troops seemed to have come from South Lancashire, those from the Fylde being called up at the end of a fortnight. The soldiers were on duty every third day and night, their provision and pay being levied on the towns in which the companies were raised.[128] Sir Thomas Fairfax, who conducted the negotiations, left the siege early in March, and after his departure the chief command seems to have devolved upon Colonel Rigby, who stayed at Ormskirk, three miles away, and came over daily to the siege.

The first advance of the Parliamentarians drove out the royalists from the Stand in the Park which they had occupied; but the besiegers seem at first to have greatly underrated the difficulty of their task, not because they expected to take the House by storm, but thinking it was so poorly provisioned that it might be easily starved into surrender. As a matter of fact, however, Lathom was well stocked with food, and for a time at least the blockade was so incomplete that supplies could easily be brought in. Moreover the difficulty of the ground for siege operations soon became apparent, and the nearer the lines were drawn to the walls the more danger was incurred from the marksmen on the Towers. The garrison was not content merely to look on at the attack but soon began to make sorties which greatly harassed the besieging force. On Tuesday, March 12, Captain Farmer led out 100 foot and the 12 horse which was all the garrison possessed, attacked the besiegers' works, and slew several of them, taking six prisoners. The following Sunday night, Captain Chisenhale sallied out from the rear gate with 30 men, and put the Parliamentarians to ignominious flight. The accounts of these sorties are probably exaggerated, and the number of the besiegers who were killed is certainly placed much too high; but the attack was not pressed with very much resolution. Much of the firing against the House was wild, and large amounts of ammunition were wasted;[129] though it is evident that a good deal of damage was done to the buildings by cannon shots. The besiegers' most successful weapon was a large mortar which was loaded with grenades or with eight pound stone bullets and did considerable execution. One shot falling into an old court destroyed most of the buildings which surrounded it; and another struck one of the Towers and broke down a large clock.

Towards the end of March a message came from the Earl of Derby to Sir Thomas Fairfax, desiring free passage for his Lady and children from the House; but the garrison realising that Lord Derby knew nothing of the provision which had been made for a siege, or of the successful defence which was being carried on, resolved to take no notice of it. A formal acknowledgment was sent to Sir Thomas Fairfax, and a messenger was sent to Lord Derby who was then at Chester, to acquaint him more exactly with the state of things in Lancashire.