The English Patient tracks the convocation of four people at an Italian villa - a nurse, a Sikh sapper, a thief, and a badly burned Englishman - who come to forge an unlikely family, and together discover the secrets of their respective pasts, and the emotional wounds they share.
Hana tends to the burned English patient in a room of their Italian villa. The nurse asks him how he was wounded, and he replies that he "fell burning into the desert" from a plane. His plane crashed in the Sand Sea, and nomadic Bedouins saw him stand up naked from the burning plane, on fire. They saved him, but he had no memory of who he is: after the accident, he knew only that he was English. At night the patient rarely sleeps, so the nurse reads to him from whatever book she finds in the library. Books are Hana's only refuge in the Villa San Girolamo, which used to be an army hospital. The villa was abandoned after the Allied victory, but there are still buried mines all over the property.
Hana is only 20 years and won't leave the English patient even though he is destined to die and the villa is unsafe. Soon, a new character emerges: a man with bandaged hands named Caravaggio, who Hana used to know. He comes to the villa and begs Hana to leave because she cannot stay with all the bombs still left underground, undefused. Hana refuses to leave the English patient.
Caravaggio and Hana go for a walk in the garden. Caravaggio allows her to loosen the bandages and change them, and Hana sees that someone removed both of his thumbs. He tells her a German nurse was called in to do it and would have removed his whole hands if the torturers hadn't suddenly heard the Allies coming. Hana says they must have heard the bombing from outside signaling that the Germans were fleeing the city.
Outside it is raining, and Hannah plays the piano in the library. She looks up, in a flash of lightning, and sees that there are two men in the room. Two soldiers - a Sikh and another man, both holding wet guns. She continues to play until she stops, nods towards them. When Caravaggio returns, he finds Hannah and the two soldiers in the kitchen making sandwiches. One of the soldiers, an Indian Sikh, sets up a tent in the garden. This is Kip, who has come to the villa to demine the property. Hana watches him bathe in the garden, and it's clear she's attracted to him.
Kip finds a large mine in a field north of the villa, and defuses the bomb with Hana's help. However, he is shaken by the experience and resents Hana because now he feels like she feels that he owes her; that he is somehow responsible for her. These feelings bring him closer to her, and soon they become lovers.
Hana sits by the English patient in his room, and he tells her that he was part of an expedition in 1930 that went searching for the lost oasis of Zerzura. There he met Katharine Clifton, wife of British aristocrat Geoffrey Clifton. Katharine was a firebrand, full of passion and moxie, and the English patient, despite his resistance to adultery, fell in love with her. Katharine somehow wanted Geoffrey to find out about the affair, but couldn't bear to tell him. Torn, frustrated, Katharine began physically assaulting her lover - leaving bruises on him from blows, cuts from flung plates and forks. He made up excuses for his wounds, and yet continued the affair, feeling disassembled by her.
Finally, Katharine told him they could never see each other again. She couldn't risk her husband finding out about them. Eventually, however, he did - long after the affair ended. When Geoffrey Clifton found out, he arranged a murder-suicide on a plane trip and crashed the plane, killing himself, mortally wounding his wife, and yet ironically leaving the English patient injury-free.
Hearing all this, Caravaggio tells Hana that he suspects that the English patient is actually Almasy, a Hungarian spy. Hana says the war is over and says it doesn't matter. Caravaggio injects the patient with more morphine and alcohol and begins to ask him questions. The patient tells Caravaggio that after crashing in the desert, he took Katharine's body to the Cave of Swimmers, where he made love to her dead body, wrapped her in parachute material, and promised to return for her. But he was arrested in El Taj by British Intelligence, and didn't return to the cave for three years. He dug up the buried plane and put Katharine inside it. He put fuel into the tank, and they began to fly in the rotted plane. Soon, however, the oil leaked onto him, the plane began to schism, and it fell from the sky in flames.
Kip flashes back to his youth. He was supposed to be a doctor, but the arrival of war meant he would join the army as an engineer - a bomb defuser. The life expectancy in his unit was only ten weeks. Kip's leader was a man named Lord Suffolk who Kip adored, but Lord Suffolk died while dismantling a large bomb. Kip left the army when he found out that people expected him to replace Lord Suffolk in position and in vision.
Hana and Kip's affair begins to cool - from lust it turns to celibacy, and soon Kip begins to just hold Hana like his mother held him. She clearly is a surrogate for his deceased mother. Caravaggio asks the English patient if he murdered Katharine Clifton. He says Geoffrey Clifton was with British Intelligence - and Caravaggio says British Intelligence knew about Almasy's affair with Katharine even when Geoffrey didn't. When Geoffrey died, British Intelligence went to capture the English patient and finally did at El Taj. Caravaggio tells Almasy that he worked for the British as a thief and that Almasy was considered a dangerous spy - all of British Intelligence had been looking for him. The English patient knows nothing of all of this and can only attest to his love for Katharine.
One day, Hana sees Kip listening to the radio on his headphones in the garden. He hears something awful, runs into the tent, grabs his rifle, and runs into the villa, into the English patient's room. He tells Almasy that the Allies have dropped the atomic bomb on Japan, and wants to kill Almasy for he is a representative of the West - the West that would create such destruction. The English patient begs Kip to kill him, but Kip doesn't. Kip leaves the villa.
At the end of the novel, Hana writes a letter to her stepmother and finally explains how her father died. He was burned, and left deserted by his men. She could have saved him, but she was too far away. The novel ends with Kip, who years later is a doctor with a wife and two children. He thinks often of Hana, who used to send him letters. Because he never replied, she finally stopped.