Returning from the Mediterranean with Letty aboard, James comes across Egyptologist Professor Dawson and his daughter Emma, who is clearly ill, adrift in a small boat. The professor has a mysterious item which he keeps in a bag and, learning that they have escaped from a ship carrying lepers, James quarantines them. However a sailor called Jimmy also falls ill. The professor throws the casket that he has been hiding, stolen from a Pharaoh's tomb, overboard upon which Emma recovers but Jimmy dies. Elizabeth discovers not only that Daniel has been cheating on her but that Samuel, who now has a daughter with Charlotte, is refusing to let William see his son.

Leaving Letty feeling adrift in their new, large country house, James sails to Belfast, persuading cash-strapped Captain Seth Burgess to cut him into his steamship line. William returns from two years abroad and instantly detects the cool atmosphere between his parents. Samuel and Charlotte make it clear to him that they want nothing to do with him but feel remorseful after William dies, saving a group of children from being trampled by a runaway horse and cart. His death also goes some way to reconciling his parents.

William's death causes a rift between Charlotte and Samuel, not helped when they learn that William left his son twenty thousand pounds. Seth Burgess is duped by the infamous tavern-keeper Paddy West into paying him for a crew to sail to New York with James. However they are not seamen but largely European immigrants, including a Count and his pregnant wife. James is reluctant to put them ashore on Ellis island but changes his mind after the count saves him from an attack by a fugitive murderer. Captain Baines recovers the money from West by arm-wrestling him.

Whilst Charlotte becomes bored with life with Samuel, James learns that Elizabeth is sailing to South Africa with a mysterious and dangerous cargo. She is in fact gun-running. James needs money for the repair of his steamer and sails after his sister, illegally using a bogus distress flag to get her to stop. He persuades her that she is in an awkward position and buys the guns from her as a job lot. However, when he tries to sell them to Major Nesbitt in South Africa, he makes a heavy loss, which amuses Captain Baines.

James takes Mr. Da Silva and his cargo of lemons to the Azores, but crew members Harris and McDade bully cabin boy Tom into helping them rob his possessions and kill the bosun when he tries to stop them. Eventually Tom does the decent thing, leading to their arrest. Samuel gives Charlotte three thousand pounds but, charmed by Seth Burgess, she gives it to him supposedly as a business investment. However he intends to buy back his ship 'The Black pearl' with it and leave her behind.

Seth Burgess obtains a contract to take China clay to Jamaica but whilst James is transporting it, Burgess elopes with Charlotte and her Onedin line shares. Whilst Samuel shows no interest in pursuing them, James offers a reward for their apprehension. Having found a baby left on her doorstep, which she hands onto the orphanage, Letty plans to open her own home for waifs and strays with the money obtained from Samuel for the sale of her factory. With Daniel now permanently in London, Elizabeth meets Charles Marston, wealthy heir to a colliery and steelworks, with whom she strikes up a business deal.

Whilst Charles Marston goes into partnership with Elizabeth to build a South American railway, Sarah accepts a marriage proposal from steamboat captain Dampier. Captain Baines sails to France with a passenger, likeable young Thomas Bullen, who saves the life of cabin boy Tom. When Bullen is recalled to England to answer a theft charge brought about by Marston, James, who dislikes his sister's new partner, and Captain Baines are pleased when Bullen proves his innocence. Unfortunately Bullen also, unwittingly, alerts them to the fact that Dampier is a penniless fortune-hunter so James pays him off to leave Sarah.

Letty faces opposition to establishing her orphanage from bigots who feel it will lower the tone of the area. Despite herself Elizabeth finds she is falling for Charles Marston and agrees to ship a cargo of wine over in time for his father's birthday. However her ship needs repairs so she gets James to do it instead. As Marston is now in his debt James gets him to persuade the lease-holder of the proposed orphanage, a family friend of the Marstons, to sell it to Letty despite the local protests. He also finds out where Charlotte and Burgess are.

James pursues Charlotte and Burgess to Cyprus where he exposes the young captain's interest in his daughter as being purely mercenary, persuading a despairing Charlotte to return home with him. Samuel is smitten by charming actress Helen Doyle and she too is fond of him whilst accepting that her father Fergus is using Samuel's acquaintance to get Sarah to finance his new play. Samuel is saddened when the Doyles' touring company moves on and makes it clear to the returning Charlotte that their marriage is over. Marston is keen to marry Elizabeth and is angry when his father approaches her asking his help in finding a wife for his son.

The Doyles return to Liverpool and Samuel declares his love for Helen but Charlotte refuses to divorce him - whilst Sarah and Fergus spend time together. Elizabeth learns that Daniel is the new ambassador to Turkey, an appointment engineered by Marston's father so that she will be obliged to leave Liverpool and join her husband. Helped by Tom, for whom he has arranged a master's apprenticeship, James tracks down Burgess, who has stolen back the ship the 'Black Pearl'. However he lets him keep the ship and returns to Liverpool, finding his house full of children following a fire at Letty's orphanage.