Partridge refused to relinquish his command when former student (but superior officer) Sylvanus Thayer was appointed to replace him as superintendent and was court-martialed for insubordination and neglect of duty. Though acquitted of serious wrongdoing, he chose to resign his commission in 1818, after having served his entire Army career at the academy. He received a pension for his service at West Point during the War of 1812, and after his death his wife received a pension as the widow of an 1812 veteran.
