On 27 July 1812, Lee received grave injuries while helping to resist an attack on his friend, Alexander Contee Hanson, editor of the Baltimore newspaper, The Federal Republican. Hanson was attacked by Democratic-Republican mob because his paper opposed the War of 1812. Lee and Hanson and two dozen other Federalists had taken refuge in the offices of the paper. The group surrendered to Baltimore city officials the next day and were jailed. Laborer George Woolslager led a mob that forced its way into the jail and removed and beat the Federalists over the next three hours. One Federalist, James Lingan, died.
Lee suffered extensive internal injuries as well as head and face wounds, and even his speech was affected. Lee later sailed to the West Indies in an effort to recuperate from his injuries. He died on 25 March 1818, at Dungeness, on Cumberland Island, Georgia.