He commanded Defense, Trumbull, and Virginia, and when blockaded at Baltimore, Maryland, took his men to join George Washington at the Battle of Trenton to aid in that key victory.

[3] Made the senior captain in the Continental Navy due to political influence, he nevertheless had an undistinguished career, never winning a victory or capturing a prize.

[4][5] Nicholson styled his flight as an "escape" in his report to Congress, and with the only witnesses confined to British prisons, he was eventually given command of Trumbull.

His home there became a meeting place for New York Democratic-Republican politicians, including followers of Thomas Jefferson and Aaron Burr.

[7] Nicholson greatly opposed Josiah Ogden Hoffman, including in relation to the Jay Treaty,[8] and Alexander Hamilton, who challenged him to a duel in 1795, and his policies.