The film begins in a coalmine in Pennsylvania in the 1876. Coal is still dug by hand and taken out on rails in wagons pulled by ponies. Pit props are improvised with timber. Conditions are always dirty, often cramped and generally unhealthy. Miners are shown with naked flames on their hats as their only light source (this is not historically accurate as flames had been enclosed since the 1820s since invention of the Davy lamp at its variables). Men are showing planting charges. This appears to be work-related but all men leave the mine and the resultant explosion destroys the mine.
Pinkerton sends James McParlan (Richard Harris) to investigate. He arrives by train in the late evening and goes to a local bar and orders a beer. He joins Dougherty and Frazier at a card table and says he is looking for work in the mine. They are suspicious and see his hands have never dug coal. They accuse him of cheating and a fight starts. Police Captain Davies (Frank Finlay) breaks up the fight and arrests McParlan. However this is just a ploy as the police know McParlan’s role. Davies explains to McParlan the problem of the Molly Maguires – and that they are named after a gang in Ireland. They need an inside man to infiltrate the pit.
McParlan rents a room from Mary Raines and gives his name as McKenna. He goes to the pit to ask for a job and is told to come back a 5 o clock in the morning on the following day. Back at the house he befriends Mary’s father.
He begins work the next day – it is back-breaking work and he is exhausted. At the end of the week he joins the long queue for pay. He is paid $9.24 however a long list is made of “deductions” including cost of explosives and cost of shovels. $9 is deducted so his pay for the week is 24 cents. Nevertheless he affords a pint of lager in the local bar (perhaps Yuengling Lager, as the brewery was nearby and many in PA still order this drink by simply requesting a “Lager”). Here Kehoe (Connery) observes him for the first time.
In church the priest condemns “last night’s actions” by the Molly Maguires – but we have not seen this action. James attends church with Mary.
Kenoe confronts James in the pit the next day and asks why he is there. A fake accident is organised where Kehoe rescues James from a huge avalanche of coal. James then gives a false confession saying he is there to avoid the law as he is a forger, and he is in hiding. He also says he killed a man in Buffalo, New York over a woman. Kehoe discusses “McKenna” with his wife and then with other miners. They do suspect that he is a spy.
After a violent football match with a rival pit, Dougherty gets in a fight with one of the rivals and is beaten up by the police. James is asked to take a revenge action and breaks a policeman’s jaw (we do not see this). The captain chastises James but he said he had to make it look real (quoting the captain regarding his earlier attack in the bar).
Kehoe and the four other ringleaders appear at the Raines house and usher old Mtr Raines away. They ask James to kneel an they make the sign of the cross. He thinks he is going to die but instead they make him a member of the Ancient Order of Hibernian. Mary chides him for joining but the next day they take a train trip to the city and go shopping. While Mary is looking at hats he has a rendezvous with the captain and gets payment for giving the names of the ringleaders.
A train of coal wagons is derailed by an explosion on the track co-ordinated by the Mollys. At a meeting of the Hibernians James is asked to put a superintendent at the Shenandoah pit out of action. Kehoe and James go to Shenandoah but are ambushed by the police. The police arrest eight men back at the pit but all men have alibis. James is taken to the captain to interview, who beats him up before he returns for realism.
By now James and Mary are in love. They go for a picnic and discuss morality.
Frazier and his wife are murdered in their bed by police (the “peelers”) in a revenge attack. At the funeral the priest shows little sympathy. Dougherty is arrested for killing the superintendent of the Shenandoah (John W. Jones), but this is a ploy to bring the real killers forward. As old Mr Raines gets the last rites the priest calls Kehoe to discuss the whole affair. At Mr Raines’ wake the Mollys meet in a back room. The wake party break into the company store and steal a suit for Mr Raines to be buried in. But Kehoe then gets carried away and starts stealing more things. He is distracted when James starts destroying bottles of alcohol with a shovel. They decide to set the store on fire.
Kehoe and McAndrew are caught red-handed as they break into the explosives store at the pit and find it is full of police.
Only at the trial do they discover James’ true identity. Mary watches in shock. Kehoe, McAndrew and Dougherty are sentenced to death. Mary explains she could cope with him as a murderer but not as a traitor.
Awaiting execution, Kehoe is visited in the death cell by James. They have a quiet and civilised conversation. Kehoe sees that James seeks absolution. He suddenly loses his temper and attacks James. He is rescued by the warders. He tells his one-time ally that no punishment short of hell can redeem his treachery. Detective McParland retorts that in that case, “See you in hell.”