Football is a part of everyday life in 1970s Ireland, as the overture and opening number (The Beautiful Game) demonstrate. It's especially important for Father O'Donnell's team, who are having their first practice on the first day of the season. The star player, John, seems to be a little more interested in one of the girls on the sidelines than he is in the priest, and as a punishment is forced to stay behind and take care of the equipment (Clean the Kit). Meanwhile, Thomas, a fervent Irish Catholic nationalist leads a group of thugs to get another boy, Del, who's an athiest, to quit the team. There's no room for someone like him on a Catholic team.

Mary, the girl John had been noticing during the practice, comes to the locker room to talk to him. Although they initially fight their attraction (Don't Like You), they soon decide to give it a try.

Time passes. John and Mary are quite serious with each other now. She asks him one evening to join her in a march for Catholic rights, but he is more interested in going drinking with his friends. Left alone, Mary is unable to understand why anyone would not love Ireland and want to make it better. Her sentiments are echoed - almost - by a girl with the rival Protestant team. (God's Own Country). John changes his mind and returns to go to the march with Mary, because she is more important to him (God's Own Country Protestant March).

The team makes it to the final, but their celebration is cut short when a group of Protestants trash the locker room. Christine and Del emerge to find the wreckage - they had been making love in hiding during the raid. Surveying the mess, they both wish all the fighting would stop so they could get on with their lives. (Let Us Love in Peace)

It comes down to the final. After the other team tied the goal on a penalty shot, John scores the winning goal (The Final). The boys celebrate at a local pub (Off to the Party, The Craic). Del comes to see Christine, but Thomas and his friends quickly remind him that he isn't welcome. Rather than causing any more unpleasantness, he leaves. Meanwhile, Ginger has finally got up the nerve to speak to Bernadette, who returns his affection (Don't Like You Reprise). They have a first, small kiss, and then she has to go, and Ginger helps Daniel home. After seeing him to his door, Ginger is about to head home himself when he's confronted by a gang of Protestant thugs. His attempt to escape is useless

Christine and Mary are discussing the previous evening at Mary's house. Mary disapproves of the relationship with Del until Christine convinces her that love knows no boundaries (Our Kind of Love). They are interrupted by John who brings the horrible news - Ginger is dead. Thomas arrives and asks John to go with them to get revenge, but he refuses - more violence won't do any good. As they comfort each other and go to the funeral, they all long for an end to the division and for a chance to live a normal life (Let Us Love in Peace Reprise).

John and Mary are getting married, and there are some nerves on all sides (The Happiest Day). When the time comes to make their vows though, there are no doubts (To Have and to Hold). Finally they are left alone in their hotel room for their first night together. Both are nervous, but together they work it out (The First Time).

In the middle of the night, the phone rings. It's Thomas, and he's in trouble. He asks for John's help. Mary doesn't want him to go, but John feels he owes it to his friend even though he doesn't agree with what he's doing. He finally finds Thomas and tells him it's the only time he'll ever do something like this. Thomas tries to explain to him why he has to do what he does (I'd Rather Die on My Feet Than Live on My Knees).

John is finally going to get his big break at the soccer trials. On her way to watch, Mary says goodbye to Christine and Del, who are moving to New York to escape the situation there. Mary figures she and John will go to England, and they talk about leaving their home (God's Own Country Reprise).

John makes a great impression and the coaches want him, but someone else wants him too - the police. Someone has tipped them off about how he helped Thomas, and he is taken to prison, before Mary even has a chance to tell him that she's pregnant (The Selection).

John is put with the other IRA prisoners. He tries to stay apart from them, but they work away at him and eventually he begins to think like them. Even Mary has trouble getting through to him. (Dead Zone)

She has her baby, a boy named Sean, and Daniel comes over to see them. While he's there, Thomas and two other IRA agents barge in and accuse Daniel of betraying John. They shoot him in the knee, crippling him. Mary is horrified and wonders if any good could possibly come out of all this violence (If This is What We're Fighting For).

John is finally released, and his first stop is to see Thomas, because he has realized that it was Thomas who turned him over to the police. After confronting him, John kills him.

Mary enters. She tries to find the man within John that she fell in love with, but he is buried too deep. John is going to England to work for the IRA. He leaves his soccer jersey and a picture of the championship team for his son (All the Love I Have).

As Father O'Donnell comes to collect Sean for the football practice, Mary hopes that the cycle of hate can be stopped with her son (Finale).