With the support of his cousin and close friend Lady Kildare, he expanded the Irish mission and established a number of Jesuit colleges.
During the Irish Confederate Wars, Nugent was active on the Catholic side of the conflict, including by providing political and financial support to Giovanni Battista Rinuccini, the papal nuncio.
On Nugent's arrival, his books and writings were stopped by the authorities in Winchester, England, and a number of people involved in transporting them were questioned.
He reconciled feuding members of his family, and locals began to bring him disputes to settle in large numbers, especially over issues regarding clandestine marriages.
He arranged for the construction of a chapel in Dublin in 1628, followed by housing for the Jesuits, who had previously been living clandestinely with friends and relatives.
Lady Kildare contributed land leased from Christ Church Cathedral, where, under Nugent's direction, a college was built for the Jesuit novitiate.
In late 1629 and early 1630, Vitelleschi's concerns proved founded, as government harassment of Catholics increased and Jesuit housing in Cork and Dublin was seized.
[2][6] In 1629, Jesuit controversialist Henry Fitzsimon returned from Belgium to Ireland, where he quickly became a source of frustration to Nugent.
On Vitelleschi's advice, Nugent avoided directly involving himself in the conflict, but his letters express strong sympathies for the Catholic side and appeal to the Pope for support.
In areas controlled by the Catholics, however, the Jesuits openly thrived, with flourishing missions in Kilkenny, Wexford, New Ross, Waterford, Clonmel, Limerick, and Galway.
Carlo Sangrio, the new vicar general of the Society of Jesus, wrote to Nugent complaining that the reports from Ireland were few and far between.
In early 1652, however, his superiors ordered him to leave Ireland, concerned that he knew too much about the Irish missions and would endanger all the Jesuits if captured.