Callon and his son are killed in a fire and the company passes to his niece, Emma. Daniel, attracted to her, wastes no time in offering his services as her business advisor. James charters the 'Star of Bethlehem' for a voyage to the West Indies with a man named Jessop amongst the crew. He is a Union man and quick to assert the sailor's rights to decent treatment. When a man falls overboard and dies, Jessop blames James, as does Anne, who annoys her husband by using his money to help the widow at an auction of his belongings.

In Liverpool Jessop sets about organizing a strike though many seamen feel they cannot afford it. When the strike finally occurs Anne, shocked by her husband's callous attitude, helps the strikers' families. James is prepared to negotiate with Jessop, brokering a separate deal giving the advantage to the Onedins and not the Callon line. However Fogarty calls in strike breakers, leading to a full-scale riot during which Robert's shop is burned down. Anne, unable to cope with James' opposition to her charitable actions, leaves him.

Anne lodges with a grateful Mrs. Jessop but initially has trouble finding work until she becomes a bookkeeper in a shop. James discovers a stowaway, Peter Thompson, whom he puts to work on the 'Charlotte Rhodes' but the boy is unused to sailing and has a bad fall. James is annoyed to discover that Peter's father is a wealthy potato merchant who, after learning of Onedin's treatment of his son, not only refuses to deal with James but also has him beaten up.

In Ireland an enigmatic woman, Miss Indigo Jones, asks James to get her damaged ship the 'Samantha', with its cargo of guano, home to Liverpool. James is suspicious that there is something wrong but, motivated by greed as usual, consents. The ship is filthy but James has it cleaned and, having bribed a relation of Albert he gets it through customs. Only then does he learn the horrifying truth. Miss Indigo has killed several crew members because they had Yellow fever, which even now may have entered Liverpool. Captain Baines attempts to reconcile the Onedins but each is too stubborn to give way.

Yellow fever hits the port. Albert is convinced James caused it by docking Indigo Jones' ship. Albert's father is to head the tribunal enquiring into the source of the epidemic and appoints Fogarty as an independent assessor of the deaths of Liverpool seaman. Fogarty takes great delight in in telling Elizabeth he will use the evidence to finish Onedin. However Albert persuades his father that James kept quiet to protect the good name of the Frazers, with whom he was associated, and James is exonerated. The outbreak starts to abate and there is a reconciliation between James and Anne when she is suspected of having the illness and he rushes to her hospital bedside.

Returning from a voyage to China, James picks up an old man floating in a life-boat. He is John Hennessy, sole survivor of a shipwreck, but when odd things start to happen the crew want to throw him overboard as a Jonah. Baines saves him but he admits that he killed the other occupant of the lifeboat in an act of self-preservation. Albert falls for music hall singer Carrie Harris, who ends up pregnant by him. She can be bought off but it casts a shadow on his marriage.

Without revealing her identity Elizabeth goes to see Carrie Harris, who is not pregnant but told Albert she was to get money from him. She knew Albert was married and this makes Elizabeth determined to leave him. Captain Baines is given command of the 'Pibroch', an old ship with a mysterious cargo. In fact it is a coffin ship, one that the owners deliberately want sunk because it is too old for service but sinking means they can claim the insurance. The ship is indeed sunk, Baines saves the crew with help from James but is barred for six months from captaining another ship.

Following the enquiry into the 'Pibroch''s scuttling, Baines is temporarily reduced to mate. The head of the board, Sir Walter Teal, asks Baines and Onedin to take his young son David as an apprentice. The boy is keen for a mariner's life and his father hopes the harsh realities will make him change his mind. James and Baines are very hard on him, which Albert notices, but James tells him he would be better occupied patching things up with Elizabeth. David ultimately proves himself as a very capable sailor and even puts in a good word for Baines with his father.

The Onedins and Albert travel to Turkey, where James is annoyed to find that Albert is about to agree to a ten year contract making steam engines for a local pasha. Albert is even considering living with Leyla, a concubine, unaware that back home a row between his wife and Daniel has ended in a kiss. When the pasha is murdered by enemies, however, Albert is implicated and the Liverpool party must flee as a nearby volcano erupts.

Anne is pregnant and Elizabeth urges James to buy a house and move out of the warehouse for the baby's sake. James comes across the immaculate but deserted ship the 'Maria da Gloria', and travels to Ireland, where it is to be the subject of a low-key auction, as it is a former slave ship but extremely fast. Daniel arrives and competes with James to buy the ship. It goes to James but he has paid more than he intended and thus cannot afford a house. However, on return to Liverpool, he is sad to find that Anne has miscarried.

Anne is pregnant and at last James buys a house for them. Sailing on the 'Lady Lazenby', Baines suffers an accident and in danger of needing his leg amputated. Onedin opposes this, believing that the leg can be saved if it is set, and he is proved right. Albert and Elizabeth prepare for divorce but ultimately decide to give the marriage another chance. Fogarty admits to Emma that he fathered Elizabeth's child but they still plan to marry.

James goes to Paris to collect an old debt, despite the fact that the city is in the hands of the Citizen Communards, and they are involved in a civil war with the rest of France.

James travels to Zanzibar, where he meets Said Ben Salim, a sheikh who asks him to take some Islamic pilgrims to Mecca. However, it soon transpires that these are not pilgrims but slaves and James puts them ashore in Africa, enabling them to return home. On his return to Liverpool he learns of an unusual challenge. He and Daniel Fogarty are to race each other to Foochow in China and back with a cargo of tea, the winner assuming the overall control of the Onedin Line. He is well and truly up for this, as is Daniel but Emma is less enthusiastic as the race is to start on their wedding day.

In Liverpool the Frazers combine to try and smuggle Jessop, who has been imprisoned and is now on the run, to Ireland. He is apprehended but they stand by him at court. The race between James and Daniel has begun, both captains having their wives on board. James reaches Foochow first but learns that Daniel aims to cut corners by using a second ship. However Daniel gets caught in the monsoons whilst Baines negotiates James' ship through them. Anne goes into labour as the Onedins approach Liverpool and James risks losing the race by breaking protocol and rushing her to the port without taking on board the pilot. However he is declared the winner but his joy is short-lived for Anne dies giving birth to their daughter.