The Northern Virginia Campaign, which includes the Second Battle of Bull Run, ends in yet another victory for the South.

McClellan resists General-in-Chief Henry Halleck's orders to send reinforcements to John Pope's Union Army of Virginia, which makes it easier for Lee's Confederates to defeat twice the number of combined enemy troops.

The Union military command in the West, however, suffers from a lack of unified command, organized by November into three separate departments: the Department of Kansas, under Major General David Hunter, the Department of the Missouri, under Major General Henry Halleck, and the Department of the Ohio, under Brigadier General Don Carlos Buell (who had replaced Brigadier General William Tecumseh Sherman).

By January 1862, this disunity of command is apparent because no strategy for operations in the Western theater can be agreed upon.

Buell, under political pressure to invade and hold pro-Union East Tennessee, moves slowly in the direction of Nashville, but achieves nothing more substantial toward his goal than minor victories at Middle Creek (January 10, 1862) under Colonel James A. Garfield and Mill Springs (January 19) under Brig. Gen. George Henry Thomas. (Mill Springs is a significant victory in a strategic sense because it breaks the end of the Confederate Western defensive line and opens the Cumberland Gap to East Tennessee, but it gets Buell no closer to Nashville.)

In Major General Henry Halleck's department, Grant had demonstrated up the Tennessee River by attacking the Confederate camp at Belmont to divert attention from Buell's intended advance, which had not occurred.

On February 1, 1862, after repeated requests by Grant, Halleck authorizes Grant to move against Fort Henry on the Tennessee.

Grant moves swiftly, starting his troops up the Tennessee River toward Fort Henry on river transports on February 2.

His operations in the campaign are well coordinated with United States Navy Flag Officer Andrew H. Foote.

The fort is poorly situated on a floodplain and virtually indefensible against gunboats, with many of its guns under water.

Because of the previous neutrality of Kentucky, the Confederates could not build river defenses at a more strategic location inside the state, so they had settled for a site just inside the border of Tennessee.

Brigadier general Lloyd Tilghman withdraws almost all of his garrison on February 5, moving them across country eleven miles (eighteen kilometers) to the east to Fort Donelson.

With a reduced crew manning the cannons, Tilghman fights an artillery duel with the Union squadron for nearly three hours before he determines that further resistance is useless.

The Tennessee River is now open for future Union operations into the South.

The federal occupation forces in Missouri soon come to regard the pro-South guerillas as common criminals rather than soldiers.

Under the orders of General Henry Halleck in March of 1862, they officially institute a policy of executing captured guerillas.

Federal forces also begin rounding up and imprisoning family members of suspected guerillas.

Guerilla leaders reciprocate by often killing the soldiers they capture, and “No Quarter” becomes a rallying cry.

Guerilla activity does not abate, and federal commanders begin harassing civilians suspected of assisting the Confederate cause by aiding the guerillas.

Some are harassed for feeding a family member home on furlough from the war.

According to some accounts, men and even young boys are often murdered by federal troops for their refusal to betray the hiding places of guerilla bands.

Beauregard plans to concentrate his forces in the vicinity of Corinth, Mississippi, and prepare for an offensive.

Johnston moves his force to concentrate with Beauregard's by late March.

The preparations for the Union campaign have not proceeded smoothly, and Halleck seems more concerned with his standing in relation to General-in-Chief George B. McClellan than he does with understanding the Confederate Army is divided and canbe defeated in detail.

Further, he cannot agree with his peer, Buell, now in Nashville, on a joint course of action.

He sends Grant up the Tennessee River while Buell remains in Nashville.

President Lincoln appoints Halleck the commander of all forces from the Missouri River to Knoxville, Tennessee, on March 11, thus achieving the needed unity of command, and Halleck orders Buell to join Grant's forces at Pittsburg Landing on the Tennessee River.

Beauregard has little concentrated strength available to oppose a southward movement by Halleck, but the Union general had showed insufficient drive to take advantage of the situation.

He had waited until he assembled a large army, combining the forces of Buell's Army of the Ohio, Grant's Army of West Tennessee, and Pope's Army of the Mississippi, to converge at Pittsburg Landing.

He had moved slowly in the direction of the critical rail junction at Corinth, in northeast Mississippi. taking four weeks to cover the twenty miles (thirty-two kilometers) from Shiloh, stopping nightly to entrench.

By May 3, Halleck was within ten miles of the city but had taken another three weeks to advance eight miles closer to Corinth, by which time Halleck is ready to start a massive bombardment of the Confederate defenses.

At this time, Beauregard decides not to make a costly defensive stand and withdraws without hostilities during the night of May 29.

Grant had not commanded directly in the Corinth campaign.

Halleck had reorganized his army, giving Grant the powerless position of second-in-command and shuffling divisions from the three armies into three "wings".

When Halleck moves east to replace McClellan as general-in-chief, Grant resumes his field command, now named the District of West Tennessee, but before he leaves, Halleck disperses his forces, sending Buell towards Chattanooga, Sherman to Memphis, one division to Arkansas, and Rosecrans to hold a covering position around Corinth.

Part of Halleck's reason for this is that Lincoln desires to capture eastern Tennessee and protect the Unionists in the region.