However, in the 16th century, the Percy family came into conflict with the crown as the staunchly Catholic family fell foul of the English Reformation which resulted in Petworth being briefly taken from them by Henry VIII, restored to them by Queen Mary I before the wider family came under scrutiny during the reign of Queen Elizabeth I. Thomas Percy, 7th Earl of Northumberland allied the family to Mary, Queen of Scots and led the 1569 Rising of the North against the Queen with the aim of deposing her and placing Mary on the throne – this failed and led to his execution for treason in 1572. His younger brother, Henry Percy, 8th Earl of Northumberland, would regain his title from the Queen after begging her mercy and was granted his freedom on the condition that the family be confined to Petworth where they could be observed by the court. The house at Petworth was therefore transformed and expanded to become the permanent home of the family with grand stables erected and a pleasure garden laid out at this time. A part of this era manor house, a 'Lost' North wing, was discovered during archaeological excavations in 2012–15 under the lawn at the front of the house having been demolished in 1692.
