Wood’s pro-Southern sympathies and racial prejudices were evident in his 1860 editorials in which he defended slavery, endorsed its expansion into the Western territories, praised the slave-based Southern culture, and opposed civil rights for free blacks.  In early 1861, he supported the right of secession and seconded Mayor Fernando Wood’s threat to declare New York a free city.  After the firing on Fort Sumter, Benjamin Wood’s disapproval of the war provoked a mob to threaten the Daily News if the newspaper did not fly the American flag above its headquarters.  He refused to give into the demand, and continued to condemn the Civil War as foolish “national fratricide.”  His strongly worded rhetoric, combined with a commitment to freedom of the press, led to problems with the government.

In May 1861, the New York City Board of Aldermen voted to rescind the status of the Daily News as the city’s official paper.  Wood sustained the journal’s position as a leading voice for the peace wing of the Democratic Party, derisively known as “Copperheads.”  Although the grand jury did not indict Wood in August 1861, the postmaster general prohibited distribution of the Daily News through the U.S. mails.  Wood employed the railroads to deliver his papers, but the federal government seized shipments in Philadelphia and Connecticut, compelling him to cease publication for 18 months.  During the hiatus he wrote an anti-war novel, Fort Lafayette; or, Love and Secession.  To his dismay, though, the book was little noticed, and its message went unheeded.  In May 1863, he renewed publication of the Daily News.

Wood’s two consecutive terms in the U.S. House of Representatives coincided with the duration of the Civil War (1861-1865).  He used his office to urge a peaceful resolution of the conflict, and to oppose all attempts at emancipation. He was a vehement critic of the draft, especially the exemption fee that allowed the wealthy to avoid military service.  However, during the bloody New York City draft riot in July 1863, he helped save the New York Times building by standing in its doorway, armed with a revolver, and instructing the rioters on the fundamental right of property.  Still, his name was linked with an alleged Confederate plot to foment the riots, although an investigation found no such evidence. 

Wood’s pro-Southern sympathies continued to be manifested in the Daily News during the Civil War.  He reprinted news from Southern papers, and in January 1864 named Phineas C. Wright as a Daily News editor.  Wright was one of the founders of the Order of American Knights, deemed by the Lincoln administration to be a pro-Confederate cabal hatching seditious plots against the Union.  Wood’s persistent anti-war rhetoric and policy proposals generated so much suspicion that the House Judiciary Committee investigated him on allegations of passing valuable information to the enemy.  Its findings were not reported, thereby leaving lingering doubts about his loyalty. 

Wood was a consistently harsh critic of Abraham Lincoln, whose policies violating civil liberties spurred the editor to label the president “a dictator.”  Yet during the 1864 presidential election, Wood also refused to endorse the Democratic candidate, General George McClellan, after the nominee repudiated the peace plank of the Democratic platform.  Wood, facing almost certain defeat at the polls, declined to run for reelection to Congress.

In early 1865, the War Department concluded that Confederate spies had been transmitting coded messages through the personal columns in the Daily News.  Threatened with arrest and court martial, Wood was forced to suspend the column.  His controversial editor, Phineas Wright, was arrested in May 1865.  Wood was not charged, but many Northerners considered the publisher to be a traitor, and were dismayed that he had not been imprisoned during the war.

Wood expressed sincere abhorrence of the assassination of President Lincoln.  The publisher initially considered the new chief executive, Andrew Johnson, to be a national embarrassment, but soon began calling for him to return to the Democratic Party.  When Johnson declined the offer, the Daily News curtailed coverage of the president and his travails.  In general, space allocated for political news in the journal decreased over the post-war years, although Wood continued to wield some back-room political power.  Poor and working-class immigrants formed his political base, electing him to the New York State Senate in 1866, and to a final term in Congress in 1880. 

The success of Wood's paper brought him considerable wealth, but gambling caused him to file for bankruptcy in 1879 and sell 43% of the Daily News stock to William J. Brown.  The federal government twice put liens on his lottery profits for failure to pay back-taxes.  In 1898, Wood sold the rest of his newspaper stock to his wife, although he continued as editor-in-chief until just before his death in February 1900.