During the reign of James II, while still a Captain, he was an active participant in the conspiracy against the King which also included his father and brother Thomas Wharton.
In August 1689 Wharton and his regiment landed in County Down as part of Marshal Schomberg's expedition and were tasked with securing Belfast whose Jacobite garrison had abandoned the town.
During the final negotiations for surrender, Wharton's troops remained poised to assault the town as an inducement for the Jacobites to agree terms.
[3] On 28 October 1689 he died of illness at Dundalk Camp, during the stand-off between the rival armies of Schomberg and James II.
After Wharton's death, his regiment came under the command of Richard Brewer and served in Flanders during the Nine Years' War.