In September of 1862, with Lee's first invasion of the North underway, Colonel Bradley Johnson and the rest of his staff from the then disbanded 1st Maryland Infantry offered their services to General Jackson for several months time while their enlisted comrades enjoyed their time in Richmond. Unable to return to their homes without facing a cell - or the rope of the gallows - they soon grew bored and homesick. Some went to join their fellows in the artillery, a few others enlisted in several Virginia units, and a large portion joined the cavalry then being formed from former elements of the 1st VA Cavalry. However, a firm portion wished to reform their old regiment, though once given the opportunity the official designation became the 2nd Maryland Infantry to avoid confusion with the original.

The company-level officers remaining, namely Captains William Murray and James Herbert, as well as Lieutenants George Thomas, Clapham Murray, and William Zollinger began recruiting both fresh recruits and veterans to quickly establish two companies and then another three shortly after. By October 18th, five hundred men had signed up with the illustrious crew and were soon assigned to General George Hume Steuart at his command in Winchester.

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After arriving, an election was held on Steuart's orders to raise staff members, and Captain Herbert was chosen to be the Major in command of the battalion. They were then assigned to General William Jones and joined the Munford's Brigade of cavalry as they neared the town of Strasburg. A sixth company helped bolster the ranks, and a seventh once Captain Goldsborough had recovered from wounds taken earlier in the war, freshly recruiting his company on the way to the rest of his men.  

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With enough numbers now to be considered a proper regiment in their right, General Jones ordered a fresh election to be held, and while the men wanted their old Colonel Johnson back, declined their offer due to other responsibilities in Richmond. Instead, Major Herbert was again promoted to Lt. Colonel, with Captain Goldsborough as his adjutant and Major of the regiment.

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After wintering in the Shenandoah Valley, and enduring blinding snowstorms as they moved from one town to the next, they had little opportunity to meet the Federals in battle, instead relegated to helping the war effort otherwise by helping transport pig iron to where it was needed. It was during this period where men would go to sleep in their blankets only to awake under a foot of snow that they found their first engagement.

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On the evening of March 25th, 1863, Captain Bond and the men of Company A of the 1st Maryland Cavalry had happened upon some Federal pickets, and when they opened fire found they had rattled the hornet's nest. In a running fight trying to reach General Jones, a courier was sent ahead to warn Jones and those in his command. The courier happened across the 2nd Maryland in his ride, and not waiting for orders Lt. Col. Herbert and his men picked up their weapons and set up a successful defensive screen against the oncoming cavalry about to attack.

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By April 21st, General Jones and General Imbodden set out to attack various points of the B&O Railroad, an important supply line for the Union in West Virginia and beyond, but decided that a pure cavalry force would be more effective for this task, so the 2nd Maryland was sent to camp at Harrisonburg. By May, elements of the Baltimore Light Artillery and 1st MD Cavalry had been detached to their area and set up on Fisher's Hill. It was during this time that Colonel Johnson in Richmond received his fateful orders to organize all the Maryland units under his command in what would become known as the Maryland Line, though it would take several weeks for the group to meet.

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In the meantime, the men of Maryland were picked up by General Steuart and subsumed under his command while joining General Lee on the way to Gettysburg. Arriving late in the afternoon, they marched around the town to join the far Confederate left at the base of Culp's Hill. Ewell in overall command of the left was ordered to attack the ridge of Culp's Hill where members of the 12th Corps had erected quick lines of breastworks among the rocks and brush. As the evening light waned, the 2nd Maryland joined the 37th, 23rd, 10th VA, and 3rd NC as they made the rough ascent, and while the Tar Heels and Marylanders were able to take the sparsely defended works, by next morning under heavy infantry assault and artillery barrage were forced back down the hill. Some of the Federal infantry attacking them at that point were fellow Marylanders. 

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After the retreat to Virginia, the 2nd was again assigned to clandestine operations and sabotage along the B&O Railroad, and while drilling at camp in Winchester were finally joined by their beloved Colonel Johnson. While reduced to battalion strength again by battle, their numbers were somewhat augmented by the arrival of Company H, originally enlisted to be cavalry, but instead assigned to the 2nd, perhaps due to a shortage of horse. 

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After several skirmishes in October of 1863 near Bristow Station, the Maryland Line was officially formed at Hanover Station along with the 1st Maryland Cavalry, and the various Artillery batteries, including the Baltimore Lights, Dement's 1st MD Artillery, and Chew's 4th MD Artillery. A general call was sent out to Marylanders in other units of the Army of Northern Virginia wishing to be part of their home state's units, but few joined given several years of fighting and camaraderie they had formed in their adoptive units. 

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Unfortunately for the Line, Dement's and Chew's battery were detached in May as they went to help Lee during the Virginia campaign, though they would never return to them. Eventually, the entire command retreated to Cold Harbor on the night of June 2nd, 1864, falling immediately to the ground exhausted without even making camp. As dawn approached their area of the battlefield drew fire from Federal pickets, and as members of Edgar's Battalion defended the salient they were sleeping behind, the men were so hardened by the battles of years past that they continued to sleep despite the whizzing of the bullets overhead. When Federal troops managed to overrun the salient and fire into the Marylanders, they awoke like a hornet's nest and drove the Federals back out of it, just in time to stop the bluecoats from turning the captured Rebel guns on them, recapturing them back while those trained on the cannons turned them back on those about to use it, firing continuously. Those not strewn about as corpses on the field in front of the breastworks were instead captured by the sleepy Rebels.

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To the dismay of the 2nd, they did not get sent back to West Virginia, instead they were attached to Frye's Brigade of Heth's Division in the reserves. They eventually reached more breastworks, now in the muddy fields of Petersburg, helping to defend the capital of Richmond. For the next few months they lived in the trenches, constantly under barrage by federal artillery, every once in a while getting the opportunity to share shots with the enemy. When Hill attempted to attack the 5th Corps near the railroad on August 18th and 19th, the 2nd were hotly engaged with their counterparts in Grant's 5th Corps, and while briefly able to get into the Federal works, were eventually forced to fall back as a third of their number was left behind as wounded, dead, and captured.

Battered, the 2nd returned to bunkering down in Battery 37, and on September 2nd moved to a new position to set up a hexagonally-shaped fort on the Peebles Farm, but as soon as they moved along with Archer's men to the Star Fort a Union attack took their hard-made fort, only for them to have to attack it themselves. On the first day the attack lasted seven hours, and after marching to a new position to the right the following morning fought for the entire rest of the next day. By the end, the 2nd lost another fifty-three man either wounded or dead, and still had not taken their own fort.

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Bedding down for the winter, the 2nd were able to avoid more disasterous combat until February 5th 1865 when they fought at Hatcher's Run, but by then the siege of Petersburg and Richmond had gained a decidedly blue advantage. During the night of April 1st, a thirty-two man section of their battalion was cut off and captured, and the rest ordered to retreat from the works. In the confusion and as they ran from the Union soldiers close behind them, the remaining were split into two squads, only reuniting on April 3rd. Only twenty-three enlisted remained but were soon found by Captain Torsch. Once the men reached the activity at Appomattox Court house, their numbers had only swollen to forty men total, which joined in surrendering under Lee.