He had also joined the Virginia militia, and in 1794 was sent as part of a detachment involved in putting down the Whiskey Rebellion. The next year he joined the regular army and served to 1801, at one point as a member of his future associate William Clark's detachment. He achieved the rank of captain before leaving the army.
He was appointed as private secretary to President Thomas Jefferson in 1801 and was intimately involved in the planning of the expedition, being sent by Jefferson to Philadelphia to be schooled in map making and other necessary skills.
After returning from the Lewis and Clark Expedition, Lewis received a reward of 1500 acres of land and was appointed governor of the Louisiana Territory and settled in St. Louis, Missouri. He was shot at a tavern called Grinder's Stand about 70 miles from Nashville, Tennessee, on the Natchez Trace, while enroute to Washington; his wrists had been cut, and he had been shot in the head and chest. Whether his death was from suicide (as is widely believed) or murder (as contended by his family) has never been conclusively determined; however, it should be noted that he allegedly attempted to jump into the Mississippi River, and drown, shortly before his death.