Lincoln is elected President, and George pays a surprise visit to Orry to apologize for what his fanatical sister said on their last visit and they resolve their differences, with Orry finally consenting to Brett marrying Billy. Ashton is still out for revenge and arranges for Billy to be attacked on the street, though it's not successful. She then turns to her lover Forbes LaMotte, Justin's nephew, to get the deed done, and Billy and Brett's wedding seems to be just the right day. Madeline overhears the plot and rushes to tell Orry, who tells her she will stay at Mont Royal and never return to Justin. Bent plots to run any blockade imposed on Southern ports. Orry travels to Pennsylvania to finish repaying George his investment in the cotton mill and realizes the full extent of the hatred that now exists. Confederate forces attack Fort Sumter and war is declared, forcing George and Orry say farewell, not knowing what the future may hold for their families or their friendship.

Orry and Charles, now officers in the Confederate Army, leave the Main family plantation for the war in Virginia. Orry, despite having been against secession, accepts a commission to brigadier general and begins to serve as military aide to Confederate President Jefferson Davis in Richmond. Meanwhile, George and Billy are in Washington, D.C., where they are officers in the U.S. Army. Billy joins the U.S. Sharpshooters regiment, while George also accepts a commission, though only to colonel, and becomes a military aide to U.S. President Abraham Lincoln.

The ebb and flow of war has begun with victories and defeats on both sides. Brett and Semiramis make it safely back to Mont Royal, after a dangerous encounter with Northern troops. When Orry hears that Justin has abducted Madeline from Mont Royal, he rescues her and they are soon married. Virgilia meets Dorothy Dix who accepts her as a nurse on the basis of Congressman Sam Greene's recommendation. Orry needs to stop the blockade runners and is almost captured by a Northern patrol. By the purest luck, he meets George on the trail. Bent has ambitions of megalomaniacal proportions and has every intention of gaining power in the South, fully expecting his new lover, Ashton, to be at his side. His scorned former paramour puts him out of business for a while. Charles is wounded and makes his way to Augusta Barclay's farm where he recuperates. At Lehigh Station, Stanley Hazard, egged on by his ever ambitious wife and against his better judgment, gets involved in shady deals.

By September 1862, the South appears to be on the verge of victory. President Lincoln wants to emancipate all slaves but recognizes he needs a victory on the battlefield before he can do so. Dissatisfied with his current commander, he sends George Hazard to sound out Gen. Ulysses S. Grant on whether he would take on overall command of the Northern forces. After the disgruntled former overseer kills a runaway slave from Mont Royal, the family decides to offer safe passage to any of their slaves who wish to leave. Soon after, Ashton arrives and is shocked to find Brett and Madeline working in the fields. She also reveals to Madeline that she knows her great secret, which she will make public unless she leaves. Virgilia is now working in a Union field hospital and is admonished by the chief nurse, Mrs. Neal, to treat all soldiers the same. Charles and Billy come face-to-face on the battlefield.

Charles and Orry set out to rescue George Hazard, who is being held at Libby Prison in Richmond. They make sure he gets back to Union lines and he makes it home for Christmas. As he recovers, however, he learns that a warrant has been issued for his arrest for selling faulty cannons to the Army. He goes after Morgan, the black marketeer, and his brother Stanley does the right thing. At Mont Royal, Brett has an unfortunate encounter with Salem Jones. Madeline has been continuing her good works in Charleston, helping those living in the shanty town and gets Rafe Baudeen's help when a group of young boys are taken to dig rifle pits for the army. Bent continues to dream of taking control of the Confederacy and gets Ashton to sleep with a contributor. Bent has a large stash of ammo and powder but Orry is soon onto him. An exhausted Charles visits Augusta Barclay.

The fighting ends with a Northern victory. Orry and George fight against each other (although not directly) in the last major battle at Petersburg; Orry is knocked out and captured...

With Madeline's school burned to the ground by the Klan, they decide to rebuild. Cooper Main has discovered phosphates on Mont Royal land and with Isabelle Hazard as an investor, begins a mining operation. The conditions of work are poor, however, and the former slaves who work there are forced into another kind of servitude when they are forced to use the company store to buy their supplies, kept in perpetual debt. In Pennsylvania, George Hazard is bereft over the loss of Constance and has become obsessed with finding Bent and exacting his revenge. He has Pinkerton's men tracking him, but they always seem to be one step behind. It takes a visit from Madeline to save him from himself. Ashton has given up prostitution and is now focusing on her new husband's piano business, obsessed with raising enough money to buy Mont Royal. Charlie Main meanwhile refuses to settle down with Willa and continues to roam the West, now as an army scout searching for Scar, who killed his friends.