On April 18, 1861 he was commissioned 1^st Lieutenant of Company H, 3^rd New York Volunteer Infantry (NYVI), a three month regiment, and fought with distinction at the Battle of Great Bethel, Virginia on June 11, 1861. On August 15, 1861 the enlisted men of the 3^rd NYVI attempted a mutiny due to the Regiment’s commitment being changed by the Government from 3 months to 2 years.[ii] 

Dissatisfied with the organization, Willoughby resigned from the 3^rd NYVI on November 2, 1861 to accept the Captaincy of a Company of Cayuga County men in the 64^th NYVI. He resigned from the 64^th NYVI on December 4, 1861 having never been mustered to accept promotion to Major of 75^th NYVI on the recommendation of his college classmate Captain Truman Fuller (Company B, 75^th NYVI).[iii] 

The 75th NYVI was mustered into service on November 26, 1861 under Colonel John Dodge (formerly Lt. Col. of the 49th New York State Militia), departed New York on December 6, 1861, arriving at Santa Rosa Island, Florida on December 15, 1861.  The Regiment was on duty there and at Fort Pickens under the command of Colonel Harvey Brown, 1st U.S. Artillery, and took part in the bombardment of Forts McRae and Barrancas, Pensacola Harbor on January 1, 1862, and the occupation of Pensacola until August 1862. During the summer of 1862 Willoughby served as Provost Marshal and Military Governor of Pensacola, Florida. On September 3, 1862 the Regiment moved to New Orleans, Louisiana, and was assigned to Brigadier General Godfrey Weitzel's Reserve Brigade, Department of the Gulf (Maj. Generals Butler, then Banks).  While attached to the Department of the Gulf, the 75th NYVI saw action at the following engagements: Georgia Landing, near Labadieville (October 26, 1862), Bayou Teche (operation against the steamer "Cotton", January 14, 1863) and siege of Port Hudson, Louisiana (March 7 to 27, 1863 and May 25 to July 9, 1863).[iv]  

On December 7, 1862 Willoughby was commissioned as Lt. Colonel of 75^th NYVI. On April 4, 1863, Willoughby assumed command of the Regiment as Colonel Merritt (promoted after Colonel Dodge resigned due to ill health) was appointed Aid-de-Camp on General Weitzel’s staff and led the 75^th on April 12 & 13, 1863 in the Battle of Fort Bisland, Louisiana. On May 27, 1863 Lt. Colonel Babcock led the 75^th during the first assault on Port Hudson, Louisiana, and with about 100 men held a log redoubt within 15 rods of the confederate rifle pits for two days, named to this day “Fort Babcock” in his honor.  During June 13 & 14, 1863, Babcock again led the 75^th in battle at Port Hudson where he was wounded seriously in the thigh during the assault on the formidable “Priest Cap” on June 14, 1863.[v]  On June 29, 1863 Willoughby returned to Regiment from New Orleans Hospital and on August 9, 1863 he was ordered to New Orleans as Provost Judge. 

On August 22, 1863 Lt. Colonel Babcock was relieved of command and brought before a court-marshal on September 4, 1863 for criticism of Generals Banks and Grover in a private letter inadvertently published in a local New York paper.  He was dismissed from the service, and did not re-enter the Army until January 28, 1864 upon the strong recommendation of several of his superior officers including General Grover.[vi] 

On February 18, 1864 he rejoined the Army and was appointed Chief of Staff to General A. L. Lee, Chief of Cavalry for the Department of the Gulf, as the 75th had been reassigned as mounted infantry.  He also served in New Orleans as Chief of Staff for Generals Arnold and Davidson, and as Superintendent of Cavalry Bureau.[vii] On August 3, 1864 Willoughby rejoined the 75th at Harper’s Ferry, Virginia after the Regiment had been transferred north to the General Sheridan’s Army of the Shenandoah.  Babcock took command of the Regiment when Colonel Merritt went to the officer’s hospital in Georgetown due to ill health.  Merritt was later detailed for duty on a commission to examine the hospitals for shirkers, and was discharged for disability on September 20, 1864.[viii] 

Lt. Colonel Babcock had command of the 75^th NYVI (320 men strong) at the Battle of Winchester, Virginia on September 19, 1864, and was wounded with a shattered leg at the head of the Regiment after two horses had previously been shot from under him.  Upon being spotted lying in the field, Major Andrew L. Pitzer (Aid-de-Camp to General Jubil Early) tended to him, and offered to send Babcock’s valuables along to his wife Nellie, which in turn he did.  After the Federal Army retook the field later in the day, Babcock was moved to a field hospital where his wounded leg was amputated by Surgeon Benedict (75^th NYVI). On October 6, 1864, after writing letters to friends and family (including a letter of thanks to Major Pitzer, and a good-by to his wife Nellie), Lt. Colonel Babcock died of his wounds at U.S. General Hospital in Winchester, Virginia.[ix]  He was brought north and is buried in Glenwood Cemetery in Homer, New York. 

The U.S. War Department posthumously brevetted Babcock Colonel and Brigadier General, U.S.V. for “conspicuous gallantry at Winchester, Virginia, September 19, 1864 when mortally wounded”.[x]  GAR Post 105 in Homer, NY was named in his honor on June 8, 1876. 

Willoughby’s two brothers were also killed during the war: Willis (1st Lieutenant of Co. G, 64^th NYVI) was killed in battle on July 2, 1863 in the Wheatfield at Gettysburg, Pennsylvania); and Lucius (Sergeant of Co. B, 9^th Minnesota Infantry) whom was captured by General Forrest’s troops during the battle of Brice’s Cross Roads, Tennessee on June 10, 1864.  He died a prisoner of war at Andersonville on September 21, 1864.  Willis is also buried in Glenwood Cemetery, and Lucius is buried at Andersonville National Cemetery (# 9474).[xi]   

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