Widowed James busies himself with work. On his new steamship the 'Anne Onedin' the passengers number coal merchant Biddulph, who arranges a shipping contract with James, and his daughter Leonora. The Callons have difficulty managing their line and sell Jack Frazer, father of Albert who is now working in Argentina, the bulk of the company whilst Daniel returns to sea. His first ship sinks due to shoddy workmanship - the rivets used to hold the boat together are inferior, or sea devils. Initially Onedin is blamed but Captain Baines discovers that the fault lay with the original builders and James is exonerated. Samuel Plimsoll, however, the 'sailor's friend', comes to Liverpool to support Robert in his bid to become a Liberal councillor, is unimpressed by James' obsession with profit.

Onedin's contract with Biddulph is jeopardised when the coal miners go on strike. Onedin eventually breaks the strike by getting some of the miners drunk, then signing them up as sailors and having them arrested if they refuse shipboard duties. Samuel Plimsoll is horrified. James Onedin also picks up a lone woman in a boat off the South American coast. Initially amnesiac she proves to be Jack Frazer's niece, Caroline Maudslay, sole survivor of an attack attack by natives on her husband's engineering expedition.

Both shipping companies are anxious to open up trade in Brazil and James learns from Caroline that her uncle has sold the 'Anne Onedin', renamed the 'Scotch Lass', to a navigation company with a view to Daniel taking it up the Amazon. Senor Braganza is anxious for his son, Jose, to become his business representative in England but the young man is only interested in tropical biology. Captain Baines goes to Portugal and drugs the lad with a view to bringing him to England but ultimately James takes him to South America, where he can study the flora and fauna.

Accompanied by Portuguese speaking Caroline and the Braganzas Onedin, Frazer, Baines and Fogarty take four ships up the Amazon with a view to establishing a coal trade with the Brazilian railways. Fogarty's men are spooked when they are attacked by natives. Ultimately Caroline knows from her understanding of the language that the locals have no intention of doing anything but fleecing the visitors and they all withdraw. However Jose Braganza is killed by natives, causing his father to terminate his dealings with Onedin.

Samuel Plimsoll returns to Liverpool to investigate the dangerous over-loading of ships. Inevitably he crosses swords with Onedin and prepares to take him to court for contravening the limit. However he comes to learn that Fogarty has actually bribed a surveyor to falsely claim that Onedin is breaking the rules to gain advantage over his rival. To show good faith Onedin invites Plimsoll on his next voyage and impresses him with his seamanship when the ship hits a storm. Annoyed by Fogarty's dirty dealings Plimsoll agrees to drop the court case providing Onedin ships carry the Plimsoll line.

Caroline's acquaintance Henry Wickham asks Onedin to smuggle valuable rubber seeds out of Brazil so that he can start a plantation in India. Onedin and Caroline set sail but they fall foul of local big-wig Ortega and, for their own safety, have to return home without the seeds. Eventually they discover that they were being used as decoys by Wickham, who, with Fogarty, set out on a separate expedition and obtained rubber seeds.

Previously the confirmed bachelor, Captain Baines falls for his landlady Mrs. Darling, and, as a favour to her, agrees to take her brother, Tom Ballantyne, on his next voyage. Tom does not approve of Baines as a suitor for his sister and animosity rises between the two men. Finally Baines strikes Ballantyne and gets into trouble as a result. Though the matter is ultimately closed it ends the captain's relationship with Mrs. Darling.

James Onedin plans to sail to Sweden with iron rails and bring home a cargo of timber for use in the Biddulph mines. Leonora, piqued at the attention James is giving Caroline, agrees to part-finance the trip and accompanies him. In Sweden Count Ericson plays hard to get, haggling for a high price for his timber but James knows he must give in else the ice floes will form and block the return voyage. Leonoras helps enormously, both by getting the count to drop his price and, when the ship is in danger of ice, donating dynamite for her father's mine, to blast its way out. However, on return to Liverpool it is Caroline whom James ends up kissing.

Captain Baines is marooned in revolution-torn Venezuela but gets permission to leave if he will take Colonel Flores, who is accompanying some art treasures to prevent the rebels seizing them. However Baines discovers that Flores is attempting to smuggle gold to America and has him arrested. Ada Mitchell, widow of the man to whom Frazer sold the 'Scotch Lass' tells James Onedin that she will give him the ship if he marries her but he refuses. He is about to propose to Caroline when he learns that Fogarty, sailing the 'Scotch Lass' home, is in severe difficulties so he rushes off to salvage the ship. When he returns Caroline turns down his proposal, feeling that any wife must come second to the shipping line.

James and Captain Baines travel to Africa to bring home wealthy young socialite William Blanshard, who has a collection of native memorabilia, as well as an African consort, Alice. Captain Baines attempts to travel up river to see if trading posts could be established but finds a huge water-fall blocking any chance of the enterprise. He contracts sleeping-sickness but is nursed back to health by Alice. Back in Liverpool Leonora learns that Caroline rejected James' marriage proposal.

Anxious to gain a contract with wealthy Zebediah Pringlehoffer, James travels to Foochow to bring home a cargo of tea. Leonora accompanies him and continues to rise in his estimation as she copes with an injury on board. James plans to bring his cargo round the Cape of Good Hope but ultimately loses the contract to Fogarty, who has vied with him in bringing home a tea cargo but used the overland railway to save time. Robert becomes a member of parliament and moves ,with Sarah, to London.

James goes to stay in London with Robert, who suggests he consider the Honorable Hugh Kernan's proposal to build the British-Mexican Railway. Captain Baines returns as a passenger from America, along with a Mr. Wallace, who has been investigating the railway as a possible investment for the Rothschild family. The ship sinks and Mr. Wallace dies. Baines survives but discovers in the dead man's belongings that Kernan's proposal is not viable, as the terrain is unsuitable for a railway. Back in London, Kernan has been seeing Leonora. It is presumed she was with him when Kernan left London shortly before Baines' news is made public. After a few days Leonora returns to London explaining she had fled to Liverpool because she could not live with a man like Kernan.

Caroline and James are returning from Baltimore, where she has been sorting out her husband's affairs. There is a new crew, hastily gathered by the shifty Bartholomew and a passenger called Draygon, escorting a thousand dollars' worth of gold bullion. On the voyage, Draygon leads the crew in a mutiny in order to gain possession of the bullion but they are thwarted by Onedin and Captain Baines. Elizabeth is in possession of a patent for hydraulic steering aboard steam-ships left her by Albert; Fogarty, now alone, is emigrating to Australia and asks her to accompany him but, on learning that he was only interested in the patent, she refuses. After his return to Liverpool, Leonora refuses James' marriage proposal in favour of his cousin, Richard.