The Civil War of the 1640s brought into question not only the divine right of kings but the powers persisting in the manorial system. Since the Cheshire gentry were equally divided between royalists and parliamentarians, the war divided families and brought distress (the brothers-in-law of the then lord of the manor, Robert Tatton, were parliamentarians, whilst he was a staunch royalist), but it also brought excitement if one believes the highly dubious account of the rector of Northenden, Thomas Mallory (a descendant of Sir Thomas Mallory of Morte d'Arthur fame). The cleric is supposed to have described how, on 25November 1643, they found parliamentarian soldiers at the church, where the east windows with the figures which included 'the form of the blessed Saint Wilfrid [were] - smashed', the font 'ground to pieces - and our fair and goodly temple laid to waste'.

The truth of the above is probably that the 'account' was written much later, perhaps even in the late 19th century. The account then goes on to say that the rector, a royalist, went to stay at the ferry house (which was being used as a parliamentarian outpost - Mallory actually went to Wythenshawe Hall) 'with a godly family, the Swindells' (the ferryman was called James Dean and he too was a member of the royalist garrison).

In the Puritan purge of High Church 'idolatry', Mallory and the rector of Cheadle, Dr. William Nicholls (who was Robert Tatton's stepfather), were ejected in September 1643. Nicholls and his wife fled to Chester (where he was later appointed Dean of Chester as successor to Mallory's father). Mallory stayed and helped to garrison Wythenshawe Hall.

With the latter and Robert Tatton, there were also Edward Legh of Baguley, a number of yeomen from the surrounding areas of Didsbury, Altrincham and Hale, and some tenants from Northenden, Etchells and Baguley. The local parliamentarian regimental commander, Colonel Duckenfield of Stockport, sent 30 soldiers under Captain Adams to besiege the hall. The siege lasted from 21 November 1643 to 25 February 1644: they finally took the hall by storm with two cannons brought from Manchester (the weather and the roads had been too bad for them to have been brought before). On the same day someone shot Captain Adams. The dubious so-called Mallory account has it as an act of revenge by a maidservant named as Mary Webb for the death of her fiance. There are depositions (i.e. statements) amongst the Tatton family papers taken by the parliamentarians at Stockport from members of the garrison and none of them mention the incident. Captain Adams was shot, but by someone unknown. He was buried at Stockport on 27 February, according to the Stockport parish register.

Robert Tatton fled to Chester, where he was appointed High Sheriff of Cheshire a few months before its surrender. He then went to support the king at Oxford, which finally surrendered to the New Model Army on 24 June 1646.

Robert was not the only heroic member of the family. In true 'secrets in her curlers' fashion, Mistress Anne Tatton smuggled letters out of Chester. She had travelled to Chester, in March 1645 with rent moneys for her husband and stepfather, who were in desperate need of money. On 10 March Sir George Booth the elder of Dunham, a prominent Cheshire parliamentarian and neighbour, gave her a safe conduct pass out of the city for herself, her servant, William Tomlinson, and two other ladies. They were stopped at Tarvin by an enemy patrol and their baggage searched. Mistress Tatton was found to be carrying letters from royalist ladies in Chester to royalist ladies in Manchester, which were of great interest to the enemy for they mentioned the movements of a royalist army marching north to relieve Chester. Mistress Tatton and her friends were sent back to Chester but were later allowed to return to their homes.