The unit spent part of April operating in Louisiana, before again crossing the Mississippi River to return to Grand Gulf.

The Confederate charge at Champion Hill captured two important battlefield features, but Union reinforcements and a lack of ammunition forced the men to retreat.

After being routed at the Battle of Big Black River Bridge on May 17, the regiment entered the defenses of Vicksburg, Mississippi.

In February 1865, the regiment was transferred to Mobile, Alabama, where it surrendered during the Battle of Fort Blakeley on April 9, ending the men's combat career.

However, Governor Claiborne Fox Jackson continued to push for secession and mobilized pro-secession elements of the state militia.

[2] Price was later reinforced by Confederate States Army troops commanded by Brigadier General Ben McCulloch.

[1] In March, Van Dorn was defeated at the Battle of Pea Ridge, giving Union forces control of Missouri.

[11] After joining the First Missouri Brigade, the regiment saw light action at the Battle of Iuka on September 19, 1862, where it suffered five casualties.

[11] At Second Corinth, the regiment was in Colonel Elijah Gates' brigade of Brigadier General Louis Hébert's division of the Confederate Army of West Tennessee.

[16] After reaching Battery Powell, the 5th Missouri Infantry fired a volley into the fortification, which cut down or dispersed the Union artillerymen still defending the position.

[23] A Union counterattack eventually swept Gates' brigade, including the 5th Missouri Infantry, from the ground they had taken;[24] the regiment suffered 87 casualties over the course of the battle.

[25] In early April, the regiment was sent across the Mississippi River into Louisiana as part of a scouting force commanded by Colonel Francis M.

[28] On April 15, Company F was part of a small force Cockrell led in a surprise attack on a Union outpost at Dunbar's Plantation.

[29] On April 17, the Missourians retreated back across the river into Mississippi, as the Union Navy had occupied New Carthage, Louisiana, threatening the security of the Confederate position.

Brigadier General John S. Bowen, Confederate commander at Grand Gulf, was tasked with delaying the Union advance at Port Gibson.

The 29th Wisconsin Infantry suffered heavy casualties, but Union reinforcements arrived, driving the Confederates back into the cover of a ravine.

Seven men of Company I of the 5th volunteered to provide a rear guard in the ravine by pretending to be a much larger force; this was accomplished by firing rapidly and shouting fake orders.

[49] The Confederate charge broke the first Union line, and recaptured a strategic crossroads as well as the cannons of Waddell's Battery.

[55] Most of the Confederates were halted, although the 1st and 4th Missouri Infantry (Consolidated) and portions of the 5th continued on in an attack, aiming for the Union supply train.

[56] Another Union brigade, commanded by Colonel Samuel A. Holmes, entered the fighting, and the Confederates were forced to withdraw.

It was on the Confederate right, between a body of water named Gin Lake and Brigadier General John C. Vaughn's brigade.

[62] After the defeat at Big Black River Bridge, the 5th Missouri Infantry entered the defenses of Vicksburg, Mississippi, where it was part of the Confederate reserve.

[63] The two Missouri regiments drove back the attacking Union soldiers after an encounter Bevier described as a "sharp conflict" and "dreadful slaughter".

[66] A Union artillery barrage damaged the Confederate defenses, sending fragments of the wooden logs used to build the fortifications flying as shrapnel.

[69] On May 27, the regiment was shifted to another point in the Confederate line, and was again moved on May 28, this time to a reserve position near a munitions storage site.

[70] By early June, the Confederate defenders of Vicksburg were running low on percussion caps, hindering their ability to fire at their besiegers.

[72] On June 25, a tunnel filled with 2,200 pounds (1,000 kg) of black powder was exploded below a point in the Confederate line known as the Third Louisiana Redan.

[77] McCown was appointed colonel of the consolidated regiment, Waddell retained his rank of major, and Bevier was transferred to Richmond, Virginia, to perform recruiting duty.

[80] On October 16, 1863, the 3rd and 5th Missouri Infantry (Consolidated) transferred to Meridian, Mississippi, before moving to Mobile, Alabama, in January 1864.

In February 1865, the regiment transferred to Mobile, where it surrendered on April 9 during the Battle of Fort Blakeley, ending the men's combat experience.