Custer arrives at his new command, the 7th cavalry, to find the men dispirited and under-prepared. He clashes with his commanders over both his status and his unit, then begins the process of turning the troop into an effective fighting force.
Custer and the 7th Cavalry are tasked with helping a cattle drive reach a fort west of Fort Hays. Both groups of men distrust the other but in the face of potential Indian attack they must learn somehow to work together.
Custer and California are out hunting with a party when Custer is presumed killed in an avalanche. As he makes his way home, he must contend with Black Foot and Sioux war parties, and possibly have to find an ally in Crazy Horse.
Custer's team is ambushed by a small group of Indians. Custer is furious the Indians knew the nature of his mission, and decides he needs to get to the bottom of how the Indians found out and who is the traitor in his unit. When the troops learn that one of their lieutenants is a Kiowa, suspicion falls on him.
Custer, having been ambushed by Indians finds himself in a desperate stand off with a strange mix of people at an old trading post. Custer is not sure if the Indians or the people at the post will be the ones to kill him.
While Custer leads a troop watching a Cheyenne hunting party, an accident inadvertently leads to a fight in which several braves are killed, including the brother of Chief Tall Knife. War is threatened, though Custer hopes to avoid it, and two visiting women--General Terry's sister and a crusading feminist journalist--are caught up in it as well.
While escorting a railroad crew through Crow territory, Custer and his men encounter resistance from a town of ex-Confederates who plan to carve out their own independent state. The former rebels have made an agreement with the Crow so they can stay on the land, but that agreement is shattered when one of the men kills the son of the Crow chief, and the chief demands that the man responsible be surrendered to him. The rebel town, Custer's troop, and the railroad crew with its intransigent leader all find themselves at odds with each other, but Custer is under orders ...
Custer is escorting a disgraced colonel to Fort Hays to be court-martialed when they are attacked by War Cloud's band. Custer decides to let their horses free and walk to Fort Hays on foot, forcing him and the disgraced colonel to depend on each other. But the colonel, who is being tried for atrocities committed against Indians, is more interested in battling Custer over who is more worthy of glory.
A British colonel arrives at the fort and announces that he needs to use some of the cavalrymen for a secret mission that has been approved by the U.S. government---to root out an Irish revolutionary who is planning to sell weapons to the Sioux as part of a scheme to blackmail the U.S. into supporting his cause. Custer and the redcoat form an instant dislike for each other, but still Custer volunteers for the mission.
Five small wagon parties have been attacked and massacred in the past month, and Custer's Seventh Cavalry is assigned to investigate. The Kiowa are being blamed for the attacks, but Custer believes they are not responsible. Complicating his efforts to find the real culprits are a bitter woman survivor of one of the attacks who thinks he's just a glory seeker, and a major sent from Washington who was a witness for the prosecution in his earlier court-martial.
Army scout Dan Samuels, being escorted to prison for delivering Army food to the Indians, escapes while seeing his pregnant wife one more time, killing one of Custer's troopers in the process. Custer, feeling responsible as he allowed the man his last visit, is determined to track him down and bring him back for trial even though he considers Dan a friend and sympathizes with him in many ways.