Shortly after his consecration, and while holding his first visitation at the castle of Killala, the bishop became a prisoner of the French army under General Jean Joseph Amable Humbert (his sons also had been briefly captured when they rowed out to view the ships), when French forces landed in support of the Irish Rebellion of 1798.
Of his experiences as a prisoner of the French he left a partial record in his private diary—23 Aug. to 15 September 1798—which was printed in William Hamilton Maxwell's History of the Rebellion of 1798, and in two letters to his brother Stephen, published in the Auckland Correspondence (iv.
In 1799 he published a more complete account of the French invasion of County Mayo in his Narrative of what passed at Killala in the Summer of 1798.
The impartiality of this work is said to have been a bar to the bishop's advancement He wrote also: He also published school editions of Tacitus and Demosthenes, and was an active contributor to the controversial theology of his day.
There appears to have been a strain of mental instability in the Stock family, as several of the Bishop's children and grandchildren suffered from serious psychological problems.