Letty has died from diphtheria caught from one of her orphans and Elizabeth has returned from Turkey to ensure the orphanage remains open. Sarah is on a Cook's tour of the world, Samuel has his own ships, bought from selling the shares William left his son Robert, as well as becoming the youngest chairman of the chamber of commerce. He divorces Charlotte and is awarded custody of the children but agrees to repay the shares in the little boy's account.

Still in Bulgaria having dropped off the disguised, fugitive Prince Alexander Onedin and Captain Baines are captured by Tsarists, a fifty thousand pound ransom being required for their freedom. By selling off some of her shares and four of her brother's ships, Elizabeth raises the money and travels to Bulgaria with Samuel to hand it over. However the captives have already been rescued by the quick-thinking Tom and James is far from grateful to his sister for her gesture, which, he claims, will ruin him.

An ancient cannon Captain Baines believes to have belonged to Henry Morgan and spirited Margarita, daughter of South American president Juarez, join James' latest cargo but on arrival in Margarita's home country James finds that her father is about to be overthrown in a revolution by his brother-in-law. When the rebels attack James and Tom help the Juarezes to escape but the president is shot by a sniper and, as the surviving trio row back to the ship under fire, the cannon comes in very handy. Elizabeth counts the financial cost of putting up ransom money for her brother.

James marries Margarita and they sail to Sumatra to establish trade in the East Indies, staying with Dutch ship-owning brothers Max and Theodore Van der Rheede. The brothers are not happy to learn that James has undercut them on a tobacco contract and the dominant Max suggests to his younger brother that they sell up and return to Europe. On the voyage home Margarita intercedes on behalf of a sailor she believes to be harshly-treated, influencing Baines to show him leniency. Back in Liverpool they find that Max has moved there ahead of them but his brother has drowned himself.

Defying the superstition that it is bad luck to set sail on a Friday, James travels to Africa and outwits a local witch doctor to establish a trading post on the Niger. However he falls out with Captain Baines, who now has his own ship, 'The Sea Spray', in the process. Back in Liverpool Margarita is mugged whilst exploring the city alone and Samuel uses his uncle's debt to pay Van Der Rheede for a warehouse in New York.

Captain Baines leaves the Onedin Line and, with Tom aboard, collects his first cargo as owner of the 'Sea Spray'. James suffers as some clients will only trust their freight to his old ship-mate and the vengeful Van Der Rheede - who is out to break him - calls in the debt sold on by Samuel, who returns from New York with a wealthy American bride. To compound matters Charlotte arrives back in Liverpool as a music-hall singer. Ultimately, though, it is Captain Baines who pays the price of pride as his ship blows up, killing Tom.

Devastated by Tom's death, Captain Baines blames Onedin for hectoring the boy into running away and joining the 'Sea Spray'. With no ship of his own he allows Van Der Rheede to bail him out but Van Der Rheede, holding Onedin responsible for his brother's death, is determined to break him and plants a stolen necklace, acquired from Betsy, a fence, on James Onedin's ship. He arranges for Betsy to be sent away and James is arrested and sent for trial. The family suspect Van Der Rheede and Elizabeth accuses him to his face but they can do nothing.

Charlotte is reunited with her father after visiting him in jail. Margarita and Samuel pursue the man suspected of planting the necklace on James' ship, only to find he is dead. However a letter arrives from Betsy, addressed to Letty, who was good to her, outlining how Van Der Rheede used her to get the necklace. Furthermore Captain Baines, now anxious to help Onedin, establishes that Van Der Rheede planted it in a chart he knew that the captain was returning to James' ship. The family confronts the Dutchman and force him to confess, whilst Elizabeth hears that Daniel is returning home to be reconciled with her.

Max Van Der Rheede is imprisoned and James is free. He beats Samuel to the contract of transporting nitrate and sets sail with his first cargo. Against his orders Margarita accompanies him. She is pregnant and eventually gives birth to a son. James is overjoyed. Elizabeth, on the other hand, receives distressing news. Daniel's ship has sunk returning to England and he has drowned, making her a widow for a second time.