In the present day, Japanese archaeologists explore tunnels on Iwo Jima. They find something in the dirt and the scene changes to Iwo Jima in 1944. Private First Class Saigo, a baker conscripted into the Imperial Japanese Army, and his platoon are grudgingly digging beach trenches on the island. Meanwhile, Lieutenant General Tadamichi Kuribayashi arrives to take command of the garrison and immediately begins an inspection of the island defenses. He saves Saigo and his friend Kashiwara from a beating for having uttered 'unpatriotic speeches' and orders the men to stop digging trenches on the beach and begin tunnelling defenses into Mount Suribachi.
Later, Lieutenant Colonel Baron Takeichi Nishi, a famous Olympic gold medali
st show jumper, joins Kuribayashi for dinner. They discuss the grim prospect of no naval support and the fanaticism their fellow officers would show. Kuribayashi evacuates the civilian population of Iwo Jima to mainland Japan. He clashes with some of his senior officers, who do not agree with his strategy of defending inland instead of the beaches; Kuribayashi believes the Americans will take the beaches quickly, and only the mountain defenses will have a better chance for holding out against the enemy.Poor nutrition and unsanitary conditions take their toll on the garrison; many die of dysentery, including Kashiwara. The Japanese troops begin using the caves as barracks. Kashiwara's replacement, a young soldier named Superior Private Shimizu, arrives for duty on the island. Saigo and his friends suspect that Shimizu is a spy sent from Kempeitai to report on disloyal soldiers. The first American aerial bombings occur shortly after, causing significant casualties. After the raid, Saigo is sickened when he sees the corpse of a friend, still sitting upright. Another casualty was Jupiter, Baron Nishi's horse, which was also killed by a bomb. The raid forces the Japanese to dig deeper into the volcanic island. The battle for Iwo Jima begins.
As the landings occur, the American troops suffer heavy casualties, but the Japanese beach defenses are quickly overcome, and the attack turns to the defensive positions on Mount Suribachi. Saigo assists the defense by carrying ammunition to machine gunners. When a Japanese machine gunner is killed by a shell from an American ship, Saigo is ordered by the company commander to use his rifle, since the machine gun is damaged. He handles it so clumsily that he is sent to retrieve some machine guns instead. While delivering the request from his company commander to the commander of the Suribachi garrison, Saigo overhears General Kuribayashi radioing orders to retreat northward. The Suribachi commander, however, ignores the order from the general and instead orders Saigo to deliver a message ordering the men of his company to commit suicide. The Japanese soldiers of Saigo's unit commit suicide with grenades, and the company commander shoots himself in the head with a pistol, but Saigo runs away and leaves the cave with Shimizu, convincing him that it is more productive to continue the fight rather than die. The two men flee to friendly lines, but they are accused of deserting Suribachi. They are about to be executed for cowardice when General Kuribayashi appears to stop the punishment, confirming that he had indeed ordered the retreat.
The soldiers from the caves attempt a futile attack against American positions, with the Japanese taking heavy losses. A wounded U.S. Marine is subsequently captured by N
ishi's men. He reveals his name to be Sam, and Nishi orders his medic to give him aid despite the Japanese's dwindling medical supplies. Despite their efforts, the Marine dies of his wounds. Nishi reads a letter the American received from his mother.As a bomb hits Nishi's cave, Nishi is badly wounded and blinded. His men bind his wounds, and Nishi orders them to another position on the island. As a last favor, he asks Lieutenant Okubo to leave him a rifle. After leaving that position, the soldiers hear a distant gunshot from Nishi's cave.
Shimizu divulges to Saigo that he had been dishonorably discharged from the Kempeitai. In a flashback, it is revealed that he was discharged because he refused to obey a superior's order to kill a barking dog. He was then reassigned to Iwo Jima. This causes Saigo's attitude towards Shimizu to soften considerably. Shimizu breaks down and fearfully asks Saigo to surrender with him.
Shimizu surrenders to a U.S. Marine patrol and finds himself in the company of another Japanese soldier who had surrendered. One of the American guards, who does not want to be burdened with POWs, later shoots them. The dead soldiers are discovered by the Japanese and Lieutenant Okubo points it out as a lesson for anyone else who wishes to surrender. Saigo, deeply saddened by his death, puts Shimizu's senninbari on his dead body.
Saigo and the remaining survivors find that Kuribayashi's cave is under attack, and a fierce battle rages. They charge through the crossfire, and lose several men, including Lieuten
ant Okubo. They enter the cave under a storm of American bullets, meeting up with Kuribayashi, who recognizes Saigo. One last attack with all the remaining men is planned. Kuribayashi orders Saigo to stay behind and destroy all the documents, including his own letters to his family. By this, Kuribayashi saves Saigo's life a third time. Kuribayashi and his remaining troops launch their final attack. Most of Kuribayashi's men are killed, and Kuribayashi is critically wounded.Kuribayashi's loyal aide Fujita drags him away from the battle. The next morning, Kuribayashi orders his aide to behead him; however, the aide is shot dead by an American marksman as he raises his sword. Saigo appears at this moment, having buried some of the documents in the cave instead of burning them all. Summoning his last reserves of strength, the very weak Kuribayashi asks Saigo to bury him so that nobody will find him. Kuribayashi then draws his souvenir M1911 pistol (In two previous flashbacks, it was revealed to be a gift from a party in the United States before the war, where Kuribayashi was given the pistol as a gift at a ceremony where he was the guest of honor) and shoots himself in the chest. Saigo carries away the dead general and buries his body.
Upon his return, Saigo finds that a patrol of American Marines have claimed Kuribayashi's pistol and Fujita's sword as war trophies. Upon seeing the pistol tucked into a Marine's belt, Saigo swings angrily and wildly at the Americans with his shovel. Too weak to fight properly, Saigo is knocked unconscious with a rifle butt and is taken on to a U.S. aid station on the beach. Awakening a while later, he glimpses the setting sun, with ships in the distance, as well as a U.S. truck, and smiles grimly.
The scene shifts back to the Japanese archaeologists who uncover the bag of letters written by Japanese soldiers on the island, never sent, that Saigo buried in 1945. As the letters fall from the bag, the voices of the fallen Japanese soldiers are heard reading from them.
