When the American Revolution began, Skene's son Andrew was arrested as Crown Point and Ticonderoga were being seized. Skene himself was returning from England; on hearing of the outbreak of the Revolution, his ship was diverted to Philadelphia. His arrival there alarmed the
Continental Congress to the extent of appointing a committee headed by
John Adams to look over his papers; after their report, he was sent to Connecticut under arrest. John Adams wrote of Skene, We have an infernal scoundrel here, a certain Col. S——, who comes over full of plans and machinations of mischief. He has had the most unreserved and unlimited confidence of
Lord Dartmouth, during the whole of the past winter, and it seems for some time before; and together with a contemptible puppy of a parson, V——, has been contriving to debauch, seduce, and corrupt New-York. After giving parole, Skene and his son lived with
Sarah Hooker at her house in
West Hartford, Connecticut. While he was there, there was some alarm when Skene's "negro" slave John Anderson was appointed "governor of the negros" by the previous incumbent. Governor
Trumbull and his council appointed a committee headed by
Jesse Root to call on Skene and examine whether this was part of some plot, which Skene denied. Skene was eventually exchanged for
James Lovell in October 1776. On his return to England in 1777 he enlisted with General
John Burgoyne's expedition and was given the rank of colonel. Burgoyne used Skene's home in Skenesborough as a headquarters in early July 1777, and Skene served Burgoyne as an advisor on local conditions and a commissary. Skene was sent along with
Baum's expedition that ended at the
Battle of Bennington to recruit Loyalists; he was sent back by Baum to hurry along the reinforcements. As the reinforcements came up, reputedly Skene hailed some American scouts with a cry of "Are you for King George?" and got his horse shot out from under him. He also may have been influential in Burgoyne's decision to cut a road from Skenesborough to
Fort Edward, perhaps with a view to improving access to his settlement. Skene was later part of the surrender of Burgoyne's army. ==Later life==