[1] Following his promotion to commander in 1855, he married and settled to work in the Navy's Japan Office in Washington, D.C., where he was serving when the Civil War broke out.

Commander Rodgers' first war assignment was to go with Commodore Louis M. Goldsborough to Gosport Navy Yard on April 20, 1861, where with other officers he was to remove Naval vessels and assets so they could not be used by the Confederates.

He was relieved by Captain Andrew Hull Foote, a more senior officer being required by the Navy to deal with the prickly Major General John C. Fremont.

The damage that the Galena suffered in the ensuing battle caused him to report, "We demonstrated that she is not shotproof", and made him disdainful of trying experiments in the fires of war.

Thereafter he supported General McClellan's Peninsula Campaign with Naval bombardment, preventing Confederate forces from overrunning the Army of the Potomac's position.

After successfully navigating her from Brooklyn to Charleston through the same storm that sank the USS Monitor, he distinguished himself during the attack on Fort Sumter in May 1863, and in capturing the Confederate ram Atlanta on June 17, 1863.

Design and construction problems with that vessel kept him occupied for the remainder of the war, though he earnestly desired a more active post.