The man with bandaged hands, Caravaggio, has been in the military hospital in Rome for over four months. He has been evasive with the doctors and nurses, refusing to tell them anything more than his serial number, which identifies him as part of the Allies. He is a war hero and they grant him his silence. He overhears the doctors talking about a nurse and a burned patient and he finally speaks to them, inquiring where the nurse is. They tell him that she and the patient are in an old, unsafe nunnery in the hills of Florence. They had tried to talk her into coming back to a safer place with them, but now that the war was over in these parts, it was impossible to force anyone to do anything anymore. The doctors tell him that the burned man talks all the time, but does not know who he is.
Caravaggio travels to the hills of Florence to find the nurse and her patient. He has known her for a long time, since she was a little girl in Toronto before the war. He remembers when she refused to have her tonsils taken out. The nurse, Hana, is surprised to see Caravaggio in her villa. He finds a bedroom and puts his things in it. She tells him that she is glad to see him, but that they will need more food now that he is here. He tells her he is unable to catch chickens like he used to, for he lost his nerve because the Germans caught him and nearly chopped off his hands. Looking at Hana, Caravaggio is reminded of his wife. He is romantically interested in Hana, but he knows she has emotionally committed herself to the dying man upstairs.
Hana asks Caravaggio if he has been a spy and he tells her he has not. He has always been a thief, and the Allies sent him to steal some documents from a room at a German party. While he was at the party in a tuxedo, a woman took a picture of him, and he knew the picture would incriminate him. That night, he snuck into the woman's bedroom and stole her camera. Though she saw him, she seemed to agree not to tell her German boyfriend on him.
Nurses such as Hana often became shell-shocked from witnessing so much death around them. Hana pinpoints her breakdown to the moment that an official delivered a letter to her telling of the death of her father. It was not long after that that she met the English patient and decided to stay in the villa to care for him. She has never learned much about him, as there has been a shyness between them that is difficult to overcome.
One night, Caravaggio finds Hana in the kitchen, half-naked and sobbing deeply. She does not want to make love to him, as she is in love with the English patient. She believes the patient is a saint who needs her to care for him. Caravaggio tries to tell Hana that it is foolish for her to throw herself away on a ghost, but she does not care. Her mind flashes back to her youth in Toronto, when Caravaggio had been her first teacher, showing her how to do somersaults when she was little. When she grew older, she trained to be a nurse. After the first three days taking care of the men wounded from the battles of war, Hana cut off her hair because it got in the way. She never looked in a mirror again. After being in the war for so long, Hana grew colder and more detached, calling all her patients "Buddy." Staying in the villa and caring for the English patient is Hana's way of escaping the war and hiding from adulthood.
Hana and Caravaggio go out for a walk at night. He lets her change the bandages on his hands, and he tells her how he was tortured. The Germans caught him jumping from a woman's window and then brought him in, handcuffed him to a table, and cut off his thumbs. When Hana and Caravaggio get back to the house, the English patient sees Caravaggio and is stunned.
Hana decides to play the old piano in the library. Outside, it is pouring rain, and two soldiers slip into the library, at first unnoticed by Hana. With their guns, they come up to the piano and listen to her play. When Caravaggio returns, he finds Hana and the soldiers making sandwiches together in the kitchen.
One major theme of The English Patient is the way the war transforms the individuals who are involved in it. All the characters that have been introduced thus far have been entirely altered by the war. Caravaggio, a former thief, has lost not only his thumbs, but also much of his youth and his identity. He can no longer steal, nor can he live any kind of happy life. He finds himself envious of those "whole" men he sees, men who can live independently and without pity. The English patient has likewise been visibly transformed by the war. Having literally lost his entire identity, he is alive only to reflect on the life he once had. Hana, too, has been irrevocably altered by her wartime experience. After having a near-breakdown, Hana stands on the cusp of adulthood, unsure whether to take charge of her life or to hide and look for shelter like a child. She chooses to postpone her decision, remaining in a villa and caring for a burned man. The war has taken a piece of each character's identity, replacing it with a scar that each now bears.
An important and recurring symbol in the novel is the Italian villa in which Hana and the English patient live. Ondaatje writes, "there seemed little demarcation between house and landscape, between damaged building and the burned and shelled remnants of the earth." Such an organic image is symbolically important to the novel. Straddling the line between house and landscape, building and earth, the villa represents both death and rebirth. War has destroyed the villa, making huge holes in walls and ceilings. Nature has returned to fill these holes, however, replacing absence with life. Such an image mirrors the spiritual death and rebirth of the villa's inhabitants.