The king formerly called men to the defence of the Crown when, upon the 22^nd of August 1642, the Royal Standard was raised at Nottingham proclaiming the king's intention to defend his crown by force. So with the relief of Hull came orders from Parliament for the Hull garrison to harry the royalists where-ever they might be found in sufficient numbers that they could be easily beaten.

Upon St. Luke's Day, 18^th October a new mayor was elected for Hull he being Thomas Raikes, the person generally regarded as being the mayor at the time of the "First Siege". The lifting of the siege allowed the contingents from the garrison of Hull to sally forth on raids into Royalist sectors and create as much havoc as possible. This culminated on the 4th October when the most impressive raid led by the undoubtedly courageous Capt. Hotham, sir John's son, resulted in the capture of Cawood Castle a mere eight miles from the walls of York.

Both Hotham's were having doubts concerning the way in which the conflict between king and Parliament was escalating. Though both were supporters of the Parliamentary cause neither held the radical views of the increasingly predominant Puritans. Sir John seems to have made several pleas for a more peaceful approach to the king suggesting that negotiation might be a better course of action than armed conflict. By the December of 1642 he had opened covert communications with the royalist commander the Earl of Newcastle by way of Sir Marmaduke Langdale who acted as intermediary. On the 22^nd February queen Henrietta Maria landed close by Bridlington Quay with troops, munitions and money to aid her husband then lodged at York. The Hotham's took this opportunity to pave a way for their defection to the king. Capt. Hotham met with both the Earl of Newcastle and the queen herself. Seeing that there might also be a chance to improve their family lot it seems that he agreed on behalf of his father and himself to defect and open the town of Hull to the Royalists in exchange for a viscountcy for Sir John, a Barony for himself, 20,000l. in money and the life governorship of Hull for father and son.

At the same time Sir John Hotham was still upgrading the town defences. One such improvement meant the demolition of a newly built, large and expensive brick house owned by Thomas Swan (gent.). The house stood "nigh without the wall of this Towne" was ordered to be burned and pulled own in order that its location close to the walls could not be used against the defenders. The 'close' adjoining the house and in which the house had stood was commanded to be cut down and "a great sconce raised & made therein for better defence of the said Towne against the enemy." The use of the word "sconce" might provide a clue to the location of the unfortunate Mr. Swan's property. According to the Oxford English Dictionary it means a "Small fort or earthwork, usually defending a ford...." There were several locations hard by the walls which would fit the definition. The two obvious ones would have been by the Beverley Gate or by the Myton Gate. This though clearly shows that the town defences were being added to at every opportunity.

Hotham's unreliability had been made known to Parliament, which manifested itself in the form of an agent named John Saltmarsh. His instructions were to solicit a confession from Sir John as to his intentions to defect and to hand Hull over to the king. Being a trusted blood relative of the Hotham's, Sir John imparted his intentions to Saltmarsh who placed his Puritanical doctrine higher than family loyalties. He reported his discoveries to Capt. Moyer of the ship Hercules who in turn passed it on to Parliament in London.

In order to circumvent any attempted change of loyalties by the father and son, the son was, together with his command, ordered to assist with the ongoing campaign in Lincolnshire. On their arrival Capt. Hotham's men soon acquired a reputation for their wanton plundering and their free quartering on the people of Lincolnshire. Hotham (junior) also re-established contact with the queen who, by then, was lodged at Newark. Matters eventually came to a head when, during a dispute over some stores, Capt. Hotham challenged Lord Grey to resolve the matter by each command fighting the other to a conclusion. During the altercation two of Hotham's guns were turned upon Oliver Cromwell. Hotham was immediately arrested and placed in Nottingham Castle. Escape was not much of a problem in those tumultuous days and by the 28^th of June father and son were re-united within the safety of the walls of Hull. During the interim Sir John Hotham had been further persuaded to defect by the appointment of Lord Fairfax as overall Parliamentary commander in the north, a position he had been eagerly anticipating for himself. Within hours of the arrival of the fugitive Capt. Hotham, a meeting was convened between Captain Moyer of the ship Hercules, Thomas Raikes the mayor, Sir Matthew Boynton and other loyal Parliamentarians. It was decided that the Hotham's had over stepped the mark once too often, consequently on the following morning a hundred men from the Hercules captured the eastern defences of the town including the castle and blockhouses with such surprise that no blood was shed. Simultaneously another group, of soldiers this time, took and occupied the western walls, gates and defences. The magazine was captured and Capt. Hotham was arrested. Parliament had previously sanctioned Boynton to take the town if in his opinion it was under threat of being handed to the king. The timing was impeccable, as on the 29^th of June, the Earl of Newcastle's troops routed those of Lord Fairfax at the Battle of Adwalton Moor. The result of this was total command of the north by the king except for Hull and the Percy stronghold at Wressle castle.

Sir John, possibly forewarned managed to escape the town with an un-mounted escort. These were soon overtaken and arrested. Sir John meanwhile had raced north to the ferry point of Stoneferry where he was unable to cross the river Hull which meant him travelling to the crossing by Beverley. His escape route had to pass through Beverley en route to his fortified family seat at Scorborough Hall. His pursuers however had taken the more direct route and achieved Beverley before him. The troops sent to arrest Hotham were commanded by Capt. Robert Legard who had warned Colonel Matthew Boynton then in charge of the small, holding garrison at Beverley of Sir John's imminent arrival. Boynton was the son of another local gentleman, Sir Matthew Boynton of Barmston who was Sir John Hotham's brother-in-law. Sir John was quickly arrested as he passed through Beverley. Upon their arrival back in Hull, all the erstwhile escapees were placed onboard the ship Hercules still commanded by Captain Moyer who quickly set sail for London before any other attempts at escape were made. Though a hall stands in the grounds of Scorborough today, the home and hall of Sir John Hotham, which stood a short distance away from the existing hall within the evident moated area, was destroyed by fire c1705.