Not really a city. It was Petersburg.
But it was the last point of protection in front of Richmond, Virginia.
By the time Lee surrendered, the Confederates were burning the cotton that lay in the streets of Richmond. This was what caused the city to burn down.
The Wilderness Campaign was a series of battles for the purpose of clearing the wilderness, before the attempt was made to try to destroy the smaller Confederate Army of Northern Virginia and capture the Confederate capital at Richmond.
When President Lincoln had appointed US General Grant as the Union's general in chief, he was given the sacred title of Lieutenant General, used only for George Washington. Grant would not be able to capture Richmond unless he first defeated the Lee led Army of Northern Virginia.
Atlanta
Montgomery
Confederate General AP Hill graduated from West Point in 1847. He was ranked 15th among his graduating class of 38 cadets. Hill saw major battle action in most of the major Eastern Theater battles including the Battle of Antietam. He was killed 6 days before Lee's surrender at Appomattox.
If you mean after the surrender at Appomattox, then I think Grant was fairly generous about it. If it was before the surrender, he would just have said "Run up the white flag, buddy boy." He had of course ended prisoner exchange as soon as he became General-in-Chief.
On April 9, 1865, General Lee surrendered his army to Lieutenant General US Grant at the Appomattox Courthouse in Virginia. This for all practical purposes ended the war. However, it would take several more weeks before Confederate forces in various parts of the South to officially surrender their armies.
General Robert E. Lee surrendered his Army of Northern Virginia to General Ulysses S. Grant the leader of the Army of the Potomac at the Appomattox Courthouse on April 9, 1865. Communications to various battle field locations were slow in these times and it would be another two weeks before Confederate General Joseph Johnston surrendered his army to General Sherman in North Carolina. And it more than a month before Confederate General E. George Kirby Smith, leader of the Army of Trans - Mississippi surrendered.
The plan for the attack on the Confederate incursion into Maryland was to follow the Rebel army. Then, assault it in order to drive it out of the North. Finding the lost General Lee order that split the Confederate army proved to not change much as Union General McClellan was slow to act. In fact he failed to save harper's Ferry from capture by Stonewall Jackson.
Confederate General Joseph Johnston had been the Army's Quartermaster General before the US Civil War. When Johnston joined the Confederacy, he was replaced by Montgomery Meigs.Both men were West Point graduates.
The ending of the long and bloody Siege of Petersburg, a last Confederate charge by General John B. Gordon, and then the final surrender of the barefoot and starving Army of Northern Virginia by Robert E. Lee, who went to meet U.S. Grant at Appomattox Court House, declaring "I would rather die a thousand deaths."
The Confederate garrison at Vicksburg.