Fearing unrest in South Africa, Daniel asks James to bring home a large amount of gold from the country - unofficially. James naturally wants his cut. Tim, a young crew member, is subjected to a crossing the line ritual during which a man falls overboard and drowns. A cargo of wool on the ship catches fire, after which it is discovered that the gold has been stolen. Tim is responsible and speaks up to Onedin about inequality. In Liverpool Robert's son Samuel returns home whilst Elizabeth's son William declares his intention to be the richest man in the port in five ...
William takes a Frazer ship out in fog and gets it in a collision with one of the Onedin ships. It is arranged that the elderly, weak Captain Oliphant should be held responsible. Oliphant later kills himself and William is filled with remorse. Elizabeth is relieved to see that he possesses some humanity. However he is seeing Charlotte, supposedly the fiancée of a dissatisfied Samuel, who wants a more active life than working in the family shop. At dinner Samuel's father Robert chokes on a bone and dies.
Samuel does not let sentiment cloud his father's death, proposing to Letty that her mill-workers make bed linen which he will sell through a catalogue for his store, though Letty drives a harder bargain than he had imagined. William is shocked to learn that the 'Indian Queen', a Frazer ship which he chartered to a Mr. Lillie without his parents knowing, was deliberately sunk, with loss of life, for the insurance money. James has his suspicions but, even with the use of a diver, cannot proved that the cargo was never loaded.
Daniel is anxious to break the Liverpool to Manchester railway's transport monopoly of the Merseyside docks and rail board. Elizabeth suggests that they use the canal system to beat the railways. Daniel is initially unresponsive but sees the prospect of steamers being used on the canals. Samuel continues to develop his idea of mail order trading. James accepts a cargo with no questions asked or papers only to find it is from the proceeds of a robbery in Manchester.
James and Sir Daniel combine to thwart William in his bid to buy the five ships belonging to elderly Captain Murchieson on behalf of devious banker Josiah Beaumont, whom Elizabeth sees as a bad influence on her son. William moves into his own flat, where he secretly sees Charlotte, though Letty finds out. Captain Baines is tricked into buying a piano to sell in Norway, but ultimately turns the situation to his own advantage.
Elizabeth clashes with Daniel over his support for the Manchester Ship Canal, which she fears will weaken Liverpool as a port. Her anger is compounded when she is approached for patronage by charismatic young orphanage director Marcus Simmons, who tells her that families are being evicted to clear the land for the canal's construction. Daniel is innocent of this fact but it enables him to expose a business partner immorally buying up land to sell at a profit to the constructors and he supports the orphanage. James travels to Africa with missionaries as passengers, ...
Letty tells James that she is pregnant and Charlotte gives William the same news. He is stunned and, as he does not love her, refuses to marry her - although she has confided in Samuel that she believes they will wed. Samuel takes the news badly and, when he and James, sailing to Ireland, come across a deserted steamer full of high explosives, feels sufficiently reckless to help James put the cargo overboard, though they are successful and claim the salvage rights. William turns twenty-one and inherits his mother's share of the Frazer yard, which he intends to sell.
James learns of Charlotte's situation but refuses permission for her to marry William, whom he regards as worthless, and sends her out of Liverpool to have her child. He also encourages Daniel to stand against the greedy Beaumont as a councillor to thwart the banker's aim to take more land for himself if elected though Elizabeth is still unhappy about her husband's support for the ship canal. Captain Baines brings home a ship from South America, whose dying captain is an old enemy of his. Baines falls for the man's wife and considers buying the ship when her husband ...
As the council election approaches, Elizabeth, equally disapproving of her husband's interest in the Manchester Ship Canal and his rival Beaumont's plan to enrich himself with his 'new' Liverpool, ensures that each hears of, and publicizes, the other's plan so that both lose the election to her candidate, Marcus Simmons. Daniel then announces that he will be standing as a Manchester M.P. James, stuck in Ireland thanks to port inspectors with vested interests, finally returns to Liverpool for the birth of his son, though the child is weak and is not expected to survive.
Newly elected to Parliament Daniel joins with Elizabeth to prevent William from selling the Frazer Line to an apparent consortium, actually a front for Beaumont. To take his mind off his son's death, James sails to Africa with Captain Baines to find diamonds, but they end up adrift in an open boat for three months. Letty never doubts that he will come back and, on his return, he gives half of the Onedin Line to Samuel, who has married Charlotte just in time for the birth of her son.