At the beginning of the 13th century, Windsor Castle was in a poor state of repair. It had been so greatly damaged by the mangonels or catapults during the Second Siege, that it was necessary for the new king, Henry III, to take up his abode in another part: the lower bailey, and not in the old Royal quarters. The repairs were carried out as quickly as possible and some alterations made the castle assume very much of its present day appearance. A chapel was built, probably on the site of Albert Memorial Chapel. The King also built a complete set of fortifications round the Lower Ward, beginning with a tower, standing probably where the Winchester Tower now is, near the west or town end of the North Terrace. This was connected by fortifications with the Curfew, Garter, and Salisbury Towers, facing the High Street and the top of Thames Street, then round to what we now know as Henry VIII's Gate. The inner space was also surrounded by the buildings where the Military Knights now live, ending at a large tower called Henry III's Tower, but known, when first built, as the Stone Tower.

Such alterations meant the spending of a great sum of money and, often, the King had to stop building until he could get more. However, at length, his fertile brain discovered a way of obtaining what he required. Men were growing restless because the King did not always act according to the Magna Carta signed by his father and the people of London, in particular, were displaying their anger. The Queen, feeling that it was unsafe to stay in London when mobs were beginning to move about the streets, shouting loudly for their rights, endeavoured to escape from her palace and ride out to Windsor. She chose the river for the first part of her journey, but the mob, seeing her in her barge, tried to sink the boat by hurling great stones into it. The Royal watermen had to turn the barge and row for dear life to the Tower of London. Later, she contrived to escape by stealth and did finally succeed in reaching Windsor Castle.

What followed must be considered an act of shameful trickery on the part of the King, who made it an opportunity for raising funds for his castle building. He had compelled the Jews to lend him money which he never intended to repay, but there came a time when they refused to lend him any more, in spite of the consequences. He also had kept back the payment of the canons and choristers of Windsor; but even then he had not sufficient money to go on with his plans.

This treatment of the Queen by the Londoners gave him the excuse he needed. The King took away the charters of London, and in this way deprived the city of its privileges. Then he sent to the Lord Mayor, whose name was FitzThomas, bidding him appear at Windsor, with forty others whom he named - men of great wealth and position - to witness the humiliation of the capital. Those who were summoned to appear before the King hesitated, knowing that the castle at Windsor had many dungeons, and fully aware that the King was in an angry mood. There came, however, letters of safe-conduct from the King, and an assurance that they should come to no harm. Relying on this, they rode out of London on the 5th October 1265. To their consternation, when they entered Windsor's castle gates, they found themselves prisoners. Instead of being put into comfortable quarters and treated with the respect due to their station, they were placed in one of the towers "with small cheer and worse lodging" and the key was turned on them.

After a while, the King set thirty-one of them free, but was exceedingly harsh with the others. Under the threat of heavy penalties and punishment, he compelled them to sign a bond for the payment of 20,000 marks (£13,333-6s-8d). It was, he said, the only way by which they could go free and thus the King got his money. FitzThomas never emerged from his imprisonment and, whether he died in the Clewer Tower dungeons or lived out a long imprisonment in the keep on the mound, we have no further information about him. It was a shameful bit of treachery and a blot on the record of a sovereign who had proved himself little better than his father, King John.