Set before and during World War II, The English Patient is a story of love, fate, misunderstanding and healing. Told in a series of flashbacks, the film is best be explained by unwinding it into its two chronological phases.
In the first phase, set in the late 1930s, the minor Hungarian noble Count Laszlo de Almásy (Fiennes) is co-leader of a Royal Geographical Society archeological and surveying expedition in Egypt and Libya. He and his English partner Madox are at heart academics with limited sophistication in the swirling politics of Europe and North Africa. Shortly after the film begins, the morale and finances of their expedition are bolstered by an British couple, Geoffrey and Katherine Clifton (Colin Firth and Kristin Scott Thomas), that joins the exploration party. The Count is soon smitten with the gorgeous and refined Katherine. Geoffrey is often away from the group tending to other matters. An affair takes wing.
The final months before the war's onset bring an archeological triumph: the Count's discovery of an ancient Saharan cave decorated with "swimming figure" paintings dating from ancient times. This period also sees the romance between Katherine and the Count rise to a sensuous peak and then seemingly fade. Katherine is plagued with the guilt of infidelity; the Count exhibits jealous streak and an impetuousness that will later haunt him.
The fall of 1939 and the war bring all excavation at the cave to a halt, and Madox and the Count go their separate ways. Geoffrey Clifton meanwhile has pieced together the outline of the affair, and seeks a sudden and dramatic revenge: crashing his plane, with Katherine aboard, into the Count's desert camp. The wreck kills Geoffrey instantly, seriously injures Katherine, and narrowly misses the Count. He manages to take Katherine into the relative shelter of the swimming figure cave, leaves her with water, a flashlight, and a fire, then begins his scorching three day walk back to Cairo and help. The mood in British-controlled Egypt has shifted since the film's start and the dazed and dehydrated Count, with his non-English name, is unable to coherently explain to military intelligence officials the plane crash and Katherine's plight. Instead he loses his temper during questioning and is thrown into military jail. By the time he is able to escape and return to the cave (with German help), Katherine is dead. And in all but a physical sense, so is the broken-hearted Count.
The film's second phase brings us to Italy and the last months of the war. The Count by now is an invalid, having been horribly burned in a plane crash of his own not long after Katherine's death. The Count is wholly dependent by this time on pain killers and the care of his French-Canadian nurse Hana (Juliette Binoche), detached from her medical unit and established in a battered but beautiful Italian convent.
The abandoned convent becomes focal point for more plot threads, some new and some unfinished from the North African phase. All are themed around love and chance, set against the backdrop of the war. Hana has seen a fiancé and a nursing friend die in the Italian campaign, and is left to wonder if her involvement with a British-Indian lieutenant will break her cycle of love and grief or simply continue it. A visitor to the convent named Caravaggio (Willem Dafoe) at first believes he has simply found another source of morphine for his habit, but then realizes the disfigured Count played a role in his own ill-starred time in Egypt and Libya. For Caravaggio has by coincidence stumbled into the wreckage of the Count-Katherine-Geoffrey love triangle, circa 1940-42. He's lost both thumbs in a grisly interrogation at the hands of the Nazis, and has since hunted down and killed those he believes responsible for his fate. He suspects the Count was part of a web of desert spying and intrigue, confronts him with news of Madox's suicide, and posits that the Count killed the Cliftons. Only the Count's full recounting of the Cliftons' crash and the Count's map dealings with the Germans (aimed at recovering Katherine) bring Caravaggio to understanding and forgiveness.
So too does Hana find reconciliation at the film's end. Her lieutenant survives a brush with death on the war's last day and her hope in love is rekindled even as he returns to India. Alas, for the Count the conclusion of the war and revelation of his secret are also the end of his story; Hana helps him die and he drifts off to join his Katherine.