On 2 July 1644 the Royalist army in the north was broken at Marston Moor. York fell two weeks later. The great Parliamentarian alliance that had won the battle dissolved into separate jobs: the Scots under Lord Leven marched north to besiege Newcastle, the Eastern Association under Manchester turned south through Tickhill and Sheffield, and the Yorkshire forces under Lord Fairfax were left to mop up the remaining Royalist garrisons scattered across the county. They began with Helmsley Castle, held by Sir Jordan Crossland with around 200 men. The castle's curtain walls were 500 years old by then, but they were maintained, and they sat above two deep ditches with a massive south barbican guarding the only practical approach. Crossland's gunpowder and grain were the question. Fairfax meant to find out how much of each he had.

Sir Thomas Fairfax took personal command of the siege in September. There is little evidence he ever brought up siege guns powerful enough to crack Helmsley's walls; the artillery that did go on to besiege Knaresborough afterwards was waiting at Helmsley first. His plan was starvation. The Royalists answered with sallies - sudden sorties out of the south gate, fast hard fights in the ditches. Somewhere in that grinding back-and-forth Sir Thomas took two musket balls in the shoulder. One version says he was leading a counterattack against a Royalist sortie when he was hit; another says a marksman in the keep took him from the battlements while he was inspecting his lines. His shoulder blade was shattered and his arm was broken. He was carried away to York. For weeks his recovery was uncertain. Had he died at Helmsley, there would have been no Naseby campaign under his banner the following summer.

By early November conditions inside the castle were failing. Crossland sent out terms. The garrison would march out with full honours of war - colours flying, drums beating, matches lit, arms loaded - and be safely escorted to Royalist-held Scarborough. The private goods of the Duchess of Buckingham, who owned the castle, must not be plundered. Prisoners on both sides would be released. And then a strange clause: the castle of Helmsley was to be absolutely demolished, with no garrison kept there afterwards by either side. It was unusual for the defenders to demand demolition - normally that was the besiegers' demand. Crossland probably wanted to make sure no Parliamentarian commander could ever hold the castle against the king again. The garrison would also wait until 16 November to see whether Prince Rupert relieved them. If not, they would surrender.

On 4 November Sir John Mallory at Skipton Castle sent a troop of horse to link up with a force from Knaresborough Castle and break the siege. On 12 November they took the Parliamentarian outposts by surprise and scattered them - briefly. The Parliamentarians rallied, counterattacked, and routed the relievers, taking nine officers and forty-four men prisoner according to the parliamentary newsbook A Perfect Diurnal. That was the end. The terms Crossland had proposed on 6 November were now accepted by Colonel Francis Lascelles on Lord Fairfax's behalf, and on 22 November Crossland marched out of Helmsley with his remaining hundred men, bound for Scarborough and Sir Hugh Cholmley's garrison. The Parliamentarians took nine artillery pieces, three hundred muskets and pikes, and six barrels of gunpowder. Then they slighted the castle as agreed, demolishing sections of the curtain wall and blowing out the eastern wall of the keep - the missing half you can still see lying in the ditch today.