After the Battle of Sharpsburg (Northerners called it Antietam, after the creek on the battlefield), Gen. Robert E. Lee withdrew his battered Army of Northern Virginia back across the Potomac River into Virginia, and began moving south. The U.S. Army of the Potomac, under Maj. Gen. George McClellan, remained in their positions near Sharpsburg for almost a month following the battle. The focus of military action in late September and early October shifted to the Western Theatre of War. On the day of the Battle of Sharpsburg, over one thousand Federal troops under Col. John T. Wilder surrendered at Munfordville, Ky. to Confederates under Gen. Braxton Bragg; the Southerners were marching north to join forces with Confederates under Maj. Gen. Kirby Smith in northern Kentucky.
Out on the Atlantic on Sept. 18, the Confederate raider Alabama went after the New Bedford, Mass. whaling fleet, sinking the whaler Elisha Dunbar. In northeast Mississippi, Confederate Maj. Gen. Sterling Price brought his force north from Tupelo in an effort to block Federals under Maj. Gen. Ulysses Grant at Corinth from joining forces with Maj. Gen. Don Carlos Buell’s troops. The two armies clashed at Iuka on the Sept. 19. The fighting was bitter and savage, and by nightfall, Gen. Price broke off the engagement, knowing that Gen. Grant had reinforcements nearby. Confederate losses numbered a bit more than 1,500 out of 14,000 engaged. Union casualties were almost 800 out of a force of 17,000.
Out in the New Mexico Territory, Col. James Carleton, formerly in command of the “California Column” which marched east to threaten the Confederates in the spring, was promoted to Brig. Gen. and put in command of the Department of New Mexico, replacing newly-promoted Brig. Gen. Edward R.S. Canby at Fort Craig. In San Francisco, citizens raised $100,000 for the relief of Federal sick and wounded. On Monday, Sept. 22, President Lincoln presented his draft of the Emancipation Proclamation to his Cabinet. While not a decisive Union victory, Gen. McClellan had stopped Gen. Lee’s army from going into Pennsylvania, and forced them to retreat to Virginia; now President Lincoln used the “victory” at Sharpsburg, Md. to release his Proclamation, which freed slaves in the states or portion of states whose people were in rebellion against the United States, as of January 1, 1863. He also called for restoration of the Union and for congressional approval of compensated emancipation.
Union troops reoccupied Harpers Ferry after the town was evacuated by the Confederates. On the Mississippi River adjacent to Randolph, Tenn., the Federal riverboat Eugene was attacked and sunk by Confederates there; in reprisal, Federals burned the town of Randolph to the ground. The same day, some 700 Santee Sioux Indians under Chief Little Crow attempted to ambush Union troops under Col. Henry Sibley near Wood Lake, Minn. Col. Sibley’s men escaped, and then turned to engage the Indians in a pitched battle. Inflicting heavy casualties on the Sioux, the Federals gave the Sioux their first decisive defeat since their uprising began in mid-August. Col. Sibley was promoted to brigadier general for this action.
On Sept. 24, President Lincoln issued a new proclamation suspending the writ of habeas corpus and providing for military trial for “all Rebels and Insurgents, their aiders and abetters within the United States.” The Office of the Provost Marshal was created by the Union Secretary of War. In Richmond, the Confederate Senate adopted the Great Seal of the Confederate States, with a representation of George Washington in the center.