As Calhoun rides on the train with General Sherman on his tour, Dave, Barnabas, and the entire population of one of the train's stops are taken prisoner by a former Confederate officer and his group, who plan to assassinate the General.

A man who sold lumber to Calhoun's railroad has disappeared, and his brother thus refuses to unload the lumber unless and until he is found to prove the sale was made. Suspecting two renegade Indians who quit just after the man left, Dave sets out to find them, along with the seller's brother. The behaviour of the owner of a trading post leads them to suspect the answers are to be found there.

Calhoun finds an eight-year-old Arapaho boy alive as the only survivor of a battle with the Shoshone. He wants to bring him back to his people, but the Shoshone want him brought to them, as he is the son and heir to the slain Arapaho chief. Calhoun fears that he will be killed if brought to them, but local townspeople, including a close friend, want to maintain the peace with the Shoshone and thus do as they ask---while others in the town want to use the incident to start a new war.

Ben has trouble to deal with when Hode Avery, a bad sort from the war, arrives in Scalplock. Plus rancher Clay Hennings is upset that the railroad is spooking his livestock and wants it to stop.

Although Calhoun discovers that the man who saved Julie and Barnabas from ambush is a former railroad engineer branded as a traitor during the Civil War, he still decides to hire him, despite Dave's objection and his own suspicions. Unfortunately, the man still has his old associates riding with him and they are all planning to steal the gold that the train is carrying.

A horse race is actually being used as a plot to defraud the people of Scalplock and in so doing destroy Calhoun's good reputation with them.

When starving Apaches leave their reservation in search of food, and encounter a brutal Cavalry commander, Ben seeks a peaceful resolution.

After Calhoun rescues a headstrong young Indian woman from two buffalo hunters who were abusing her, he asks her to be his scout through dangerous terrain on his way to meet with a Sioux chief. She agrees, until she learns that he plans to negotiate putting the railroad through Sioux territory.

When Calhoun's railroad is given the contract to haul for a mining company, it effectively puts the owner of the old coach freight line, who had the contract before, out of business. The freight company owner's inept sons decide to get back at Calhoun by robbing the railroad of the mining company payroll, and they hire a ruthless gunman to help them.

Ben Calhoun is forced into a business transaction with conman Preston Webb. When he joins fellow grifter Helen Garth into convincing the locals of a machine that finds gold Calhoun and his friends endeavour to expose them.

Bounty hunter McCoy will stop at nothing to capture a murderer. Dave faces a dilemma, knowing the man's location but having promised a woman to keep it a secret.

Ben puts himself in the center of a conflict when he decides to help French monks establish a vineyard. But trapper Ike Bridger and his friends see it as prime beaver habitat and are unwilling to give it up without a fight.

The BPS&D's telegrapher plans to assist his three brothers in dynamiting the railroad and robbing the payroll it's carrying, until he learns that his wife and son are riding the train as well.

Ben decides it's payback time when he encounters two card sharps who swindled him out of $10,000 for a worthless hill. Ben takes them on in a poker game for which he has a special strategy.

Calhoun is puzzled as to why two mortal enemies, a man and a woman, are refusing to sell him a right-of-way for the railroad because of a mine that everybody is sure is worthless.

While the train is stopped in the town of Banner, where Calhoun is making a major business deal with town founder Big Jim Banner, Barnabas is attacked by Banner's son, who thinks Barnabas is one of the Claiborne boys with whom the Banners have a major feud. At first it seems to be a mistake, until Barnabas meets Jeff Claiborne, who looks just like him. Soon Barnabas, who was raised as an orphan, starts to believe that he may be a Claiborne as well.

With Calhoun away, the train is taken over by a group of ruthless outlaws who demand that Dave turn over a large fortune in bonds that is being delivered. Dave tells them that they will have to wait for Calhoun to return with them, but that is a delaying tactic as Calhoun will not be back that soon and Dave may have to resort to other plans to save the lives of the crew and passengers.

Calhoun is under orders from President Grant himself to safely transport Pierre Le Druc, an associate of Mexico's deposed puppet emperor Maximilian, to a meeting with his French countrymen on the west coast. But Le Druc is a ruthless killer, and a Mexican general is also pursuing the train to capture Le Druc and bring him back for trial.

Calhoun wins a high stakes poker game against outlaw gambler Dan Patrick. But Patrick says he does not have the money on him, and offers a beautiful young Spanish noblewoman as collateral. Calhoun agrees to leave the young woman with Barnabas as he goes with Patrick to retrieve the money. But Patrick has no intention of keeping his end of the bargain.

Calhoun's acquisition of a right-of-way for the railroad is threatened when he takes the side of allowing a band of Indians---mostly old people, women, and children---to go through it on their way back from the reservation to their ancestral home. The townsmen who agreed to the right-of-way do not want them to cross it, and insist that Calhoun keep them only on the narrow strip he owns or forfeit it, and hence lose the railroad.

Calhoun realizes that four members of an outlaw gang have surreptitiously boarded the train. But he decides to not let them know he is on to them until he knows their plan, and can devise one of his own to stop them.

Calhoun decides to go into the rugged Apache country hills for a fight to the death against Cougar Man, an Apache who has killed five of Calhoun's men, and who believes himself cursed to kill as many men as possible until he himself is killed.

Calhoun must transport an Army unit which has captured the renegade Sioux chief War Cloud and is bringing him to stand trial for numerous murders. This comes at a bad time for Calhoun, as he is hoping to impress another passenger, a wealthy banker whom he hopes will agree to a loan for the railroad. The banker's daughter believes War Cloud is being mistreated. But a man who lost his family in one of War Cloud's raids plans to make sure the Indian dies long before he arrives at the fort, and is willing to fight Calhoun to make sure of it.

Ben needs the right of way for his railroad in a near ghost town. But a dark secret is being kept by the last of the citizens and they would rather Ben is killed than have it revealed.

Calhoun learns from Dave and Barnabas that all of the railroad's crew has been lured away by the promise of gold from a nearby mine. Actually, it is all part of a plot to lure Calhoun away in the hope of stealing the railroad.