It is 1993 and the first steps in a tentative peace process between the British governments and the Irish paramilitary organizations, the IRA and the Irish National Liberation Army, who go by the acronym INLA.
On the island of Inishmore, Davey has found a black cat dead at the side of the street. He takes it to his neighbor, Donny's, house, and Donny accuses him of killing the cat himself with his mother's motorcycle. Davey denies it, and Donny tells him that the cat was called Wee Thomas and that he belongs to his son, Padraic. This terrifies Davey because Padraic has a violent temper and has been kicked out of the IRA for being too radical. He loves his cat more than life itself. Donny tells Davey that if he admits to killing Wee Thomas then he will keep his name out of it, and Davey reluctantly agrees. Donny calls Padraic and tells him that Wee Thomas is off his food and not feeling good, hoping that this will prepare him for worse news when he gets home.
The call interrupts Padraic as he is torturing a drug dealer named James whom he has hung upside down from the ceiling of a warehouse. He dissolves into tears on hearing the news about Wee Thomas. James, overhearing the conversation, tells him that it might be ringworm, which is easily cured. When his cat had ringworm he gave him medication wrapped up in cheese and it cleared up quickly. Padraic realizes that James loves his cat and this changes his view of him. He cuts him down from the ceiling and gives him his bus fare home.
Davey is shot in the cheek with an air rifle brandished by his militant sister Mairead. She is sixteen and has recently shot out the eyes of twenty cows as an act of terrorism against farmers. She loves Padraic, the INLA and her cat, Sir Roger. She wants to be a terrorist and thinks of nothing else. Donny tells Davey to find a black cat in the street that they can pass off as Wee Thomas but Davey comes up empty handed. He takes Mairead's cat instead, and they plan to dye his orange fur black using boot polish. They drink as they work and so the task does not move very quickly or successfully.
They receive a visit from Padraic's friend Christy, a tall man with a patch over one eye. He is accompanied by two INLA associates, Brendan and Joey. They are on Inishmore to assassinate Padraic, whom the INLA leadership feel is a liability to them. Christy came up with the idea of killing Wee Thomas because he knew it would get Padraic back to Inishmore quicker than anything else. Their conversation is overheard by Mairead who has been roped into the feline bait and switch by Donny.
Donny and Davey fall asleep, having drunk too much and not finished dying the cat. In the morning, Mairead goes to meet Padraic at the dock, to tell him that Wee Thomas is doing much better. She flirts a little but is mocked and rebuffed, although Padraic does kiss her exuberantly on hearing that his beloved cat is feeling better. When they arrive at the house, Padraic goes inside to find his father and Davey asleep next to a partially dyed cat that smells of boot polish. He ties them up so that he can get to the bottom of what has happened. He shoots the decoy cat. Donny admits that Wee Thomas has been killed but swears he doesn't know how it happened. They are interrupted by Christy and his cohorts bursting into the room and dragging Padraic outside. When they hear three shots, Donny and Davey believe their nightmare is over, but to their surprise they see Christy, Brendan and Joey come back into the house, bloodied, with their eyes shot out. Mairead, aware that they were trying to kill Padraic, was waiting for them. She follows Padraic into the house. Padraic shoots each man, and Christy tells him that he is sorry for killing his cat, which enrages Padraic all over again. He drags Christy into the other room to torture him. He asks Mairead to join him in his new terrorist splinter group and she agrees.
That evening, Padraic uses Christy's mutilated body as a seat as he holds the body of Wee Thomas to him. Donny and Davey are miraculously still alive because they are needed as a clean-up crew to dismember the bodies and dispose of them so that they cannot be identified. Padriac asks Mairead to marry him and she accepts.
Before the newly-engaged couple leave again, Mairead goes into the bathroom to clean the blood off her skin. She returns shortly afterwards, holding Sir Roger's dead body. She kisses Padraic and as he sinks into the kiss and relaxes she shoots him in the head with one of his own guns. She tells Donny and Davey to clean up the mess and proclaims herself the Lieutenant of Inishmore.
The following day, Donnie and Davey see a black cat come into the house and realize that Wee Thomas is alive and well. Christy killed another black cat in error, and the un-neutered Wee Thomas was out gallivanting all night. They are furious with him at first because four people and two cats have died because of his late night wandering but they soon forgive him and put cereal into his bowl for his breakfast.
