Halleck served as the General-in-Chief of the Armies of the United States from 1862 to 1864, and then became Chief of Staff for the remainder of the war when Ulysses S. Grant was appointed to that position.

The only operation in which Halleck exercised field command was the so-called siege of Corinth in the spring of 1862, a Union victory which he conducted with unnecessary caution, which allowed the Confederate force to escape.

In July 1862, following Major General George B. McClellan's failed Peninsula Campaign in the Eastern Theater, Halleck was promoted to general-in-chief.

Young Henry detested the thought of an agricultural life and ran away from home at an early age to be raised by an uncle, David Wager of Utica.

[4] After spending some time as a member of the teaching staff at the academy, and a few years improving the defenses of New York Harbor, he wrote a report for the United States Senate on seacoast defenses, Report on the Means of National Defence, which pleased General-in-Chief Winfield Scott, who rewarded Halleck with a trip to Europe in 1844 to study European fortifications and the French military.

[5] Returning home as a first lieutenant, Halleck gave a series of twelve lectures at the Lowell Institute in Boston that were subsequently published in 1846 as Elements of Military Art and Science.

[6] His work, one of the first expressions of American military professionalism, was well received by his colleagues and was considered one of the definitive tactical treatises used by officers in the coming Civil War.

He spent several months in California constructing fortifications, then was first exposed to combat on November 11, 1847, during William Shubrick's capture of the port of Mazatlán; Lt. Halleck served as lieutenant governor of the occupied city.

The California State Military Museum writes that Halleck "was [at the convention] and in a lone measure its brains because he had given more studious thought to the subject than any other, and General Riley had instructed him to help frame the new constitution."

During his political activities, he found time to join a law firm in San Francisco, Halleck, Peachy & Billings, which became so successful that he resigned his commission in 1854.

He built the Montgomery Block, San Francisco's first fireproof building, home to lawyers, businessmen, and later, the city's Bohemian writers and newspapers.

He was a director of the Almaden Quicksilver (Mercury) Company in San Jose, president of the Atlantic and Pacific Railroad, a builder in Monterey, and owner of the 30,000 acre (120 km2) Rancho Nicasio in Marin County.

[7] He was assigned to command the Department of the Missouri, replacing Frémont in St. Louis on November 9, and his talent for administration quickly sorted out the chaos of fraud and disorder left by his predecessor.

The pugnacious Grant had just been repulsed at the minor, but bloody, Battle of Belmont but had ambitious plans for amphibious operations on the Tennessee and Cumberland Rivers.

However, under pressure from President Lincoln to take offensive action, Halleck reconsidered and Grant conducted operations with naval and land forces against Forts Henry and Donelson in February 1862, capturing both, along with 14,000 Confederates.

Halleck also cited rumors of renewed alcoholism, but then restored Grant to field command – pressure by Lincoln and the War Department may have been a factor in this about-face.

Grant, not yet aware of the political maneuvering behind his back, regarded Halleck as "one of the greatest men of the age" and Maj. Gen. William T. Sherman described him as the "directing genius" of the events that had given the Union cause such a "tremendous lift" in the previous months.

[12] This performance can be attributed to Halleck's strategy, administrative skills, and his good management of resources, and to the excellent execution by his subordinates – Grant, Maj. Gen. Samuel R. Curtis at Pea Ridge, and Maj. Gen. John Pope at Island Number 10.

[16] In the aftermath of the failed Peninsula Campaign in Virginia, President Lincoln summoned Halleck to the East to become General-in-Chief of the Armies of the United States, as of July 23, 1862.

[4] Lincoln hoped that Halleck could prod his subordinate generals into taking more coordinated, aggressive actions across all of the theaters of war, but he was quickly disappointed, and was quoted as regarding him as "little more than a first rate clerk.

[17] In Washington, Halleck continued to excel at administrative issues and facilitated the training, equipping, and deployment of thousands of Union soldiers over vast areas.

A telling example of his lack of control was during the Northern Virginia Campaign of 1862, when Halleck was unable to motivate McClellan to reinforce Pope in a timely manner, contributing to the Union defeat at the Second Battle of Bull Run.

"[19] In Halleck's defense, his subordinate commanders in the Eastern Theater, whom he did not select, were reluctant to move against General Robert E. Lee and the Army of Northern Virginia.

And despite Lincoln's pledge to give the general in chief full control, both he and Secretary of War Edwin M. Stanton micromanaged many aspects of the military strategy of the nation.

Halleck wrote to Sherman in February 1864, "I am simply a military advisor of the Secretary of War and the President, and must obey and carry out what they decide upon, whether I concur in their decisions or not.

However, the 1864 Red River Campaign, a doomed attempt to occupy Eastern Texas, had been advocated by Halleck, over the objections of Grant and Nathaniel P. Banks, who commanded the operation.

[30]British general and military historian J. F. C. Fuller described Halleck as "a cautious, witless pedant who had studied war, and imagined that adherence to certain strategical and tactical maxims constituted the height of generalship.

Instead, by taking so long to move from Pittsburg Landing to Corinth, Halleck allowed the Confederates to escape, then chose to break up his army into small pieces and spread them around the Western theatre.

Lincoln's Secretary of the Navy, Gideon Welles, who kept a diary throughout the war, said of him "Halleck originates nothing, anticipates nothing to assist others; takes no responsibility, plans nothing, suggests nothing, is good for nothing.

[39]After Grant forced Lee's surrender at Appomattox Court House, Halleck was assigned to command the Military Division of the James, headquartered at Richmond.