The film begins in the summer of 1876, introducing Captain Nathan Algren (Tom Cruise), a disenchanted ex-United States Army captain and an alcoholic, who is traumatized by his past experiences fighting in the Civil War and the Indian Wars. In the years following his army service, Algren makes his living by relating war stories to gun show audiences, an experience which further hampers his mental state. Fed up with Algren's perpetual drunkenness, his employer fires him, forcing Algren to accept an invitation by his former commanding officer Lieutenant Colonel Bagley (Tony Goldwyn), whom Algren deeply hates and blames for his waking nightmares. Bagley approaches him with an offer on behalf of a Japanese businessman, Mr. Omura (Masato Harada), to help the new Meiji Restoration government train the new Western-style Imperial Japanese Army. Assisting them are Algren's old army colleague Sergeant Zeb Gant (Billy Connolly) and Simon Graham (Timothy Spall), a cynical British translator with a deep interest in the samurai.

Under the command of Bagley, Algren trains a conscripted army of peasants in handling a rifle. Before they can be adequately trained, Katsumoto (Ken Watanabe) attacks a railroad outside his province, to protect.Bagley orders Algren to lead the inexperienced conscripts to engage Katsumoto. Algren protest and in a demonstration, illustrates the army's inexperience and inadequate training. Despite this, Bagley sends his troops anyway. During the battle, the conscripted peasants panic, ignore their commanding officers and fire too early, and thus their shots fall short. Samurai swarm the wholly-unprepared army, routing them in seconds, killing Gant and forcing Bagley to withdraw from the field. Algren is able to cut down several samurai using his experience as a cavalry trooper with the Sabre and revolver until he is knocked off his horse when he is distracted by a samurai on horseback charging at him whilst a foot soldier with a spear advances on his horse causing it to fall. But he refuses to give in and manages to fend off several samurai with a broken spear embroidered with a flag depicting a white tiger. The flag on the spear reminds Katsumoto of a vision he experienced during meditation, of a white tiger fighting off his attackers. Katsumoto's brother-in-law, the red-masked samurai Hirotaro who shortly before gave the killing blow to Gant, prepares to deliver a killing blow to the fallen Algren; however, Algren refuses to yield and picks up a spear, fatally stabbing Hirotaro through the neck. Believing what he has witnessed to be an omen, Katsumoto prevents his warriors finishing off the wounded Algren and takes him prisoner. Algren is taken to an isolated village, where he gradually recovers in a house belonging to Hirotaro's family, including his widow Taka, her two sons, and Katsumoto's son, Nobutada (Shin Koyamada).

Over time, Algren overcomes both his alcoholism and the nightmares of his traumatic past, and sharpens his mind through practice of bushido, the way of the samurai. He confides to his journal that he has never felt as entirely at peace as he has among Katsumoto and his people. Despite lingering fidelity to Hirotaro, Taka develops romantic feelings for Algren, particularly when she notices his budding fatherly relationship toward her children. Algren studies swordsmanship under skilled swordmaster Ujio (Hiroyuki Sanada) and becomes fluent in Japanese by conversing with the local residents; in doing so, he earns their respect. One night, as the people watch a comic play, a group of ninja assassins attack the village. Algren wins the respect and admiration of the samurai by saving Katsumoto's life when the assassins fire crossbow bolts and shuriken at Katsumoto, killing the actor next to him, as well as taking up a sword and joining the battle. The samurai succeed in defeating the ninjas, but with many losses. Though Katsumoto does not confirm it, Algren deduces that the attack was ordered by Omura.

In spring, Algren is taken back to Tokyo. There he learns that the army, under Bagley's command, is now better organized and outfitted with howitzers and Gatling guns from the United States. Omura offers to place Algren in command of the army if he agrees to crush the samurai rebellion, but Algren declines. In private, Omura orders his men to kill Algren if he attempts to warn Katsumoto of their intentions. At the same time, Katsumoto offers his counsel to the young Emperor, to whom he was once a teacher. He learns that the Emperor's hold upon the throne is much weaker than he thought, and that he is essentially a puppet of Omura. When Katsumoto refuses to observe new laws that forbid samurai to publicly carry swords, he is arrested and confined to his quarters in Tokyo. Anticipating an assassination attempt on Katsumoto, Algren heads directly for his quarters but is ambushed by Omura's men; Algren narrowly escapes death through judicious use of the martial arts he learned in Katsumoto's camp. With the assistance of Ujio, Nobutada, and Graham, Algren frees Katsumoto from custody. During their flight, Nobutada is mortally wounded and stays behind to aid his father's escape; Algren looks on as a mortally wounded Nobutada charges their foes, only to be cut down by volleys of gun fire.

Katsumoto is still mourning the loss of his son when he receives word that a large Imperial Army unit, commanded by Omura and Bagley, is marching out to engage the samurai. A counter-force of samurai, numbering only 500, is rallied. Algren makes a reference to the Battle of Thermopylae in which a small army of 300 Spartans fought against a much larger opposing force of roughly over 250,000 Persians (Algren claims it was against 1 million) by using the terrain and the enemy's overconfidence to their advantage; Algren surmises that a similar tactic would reduce the effectiveness of their enemy's artillery. On the eve of battle, Algren is presented with a katana of his own. Taka also gives him her dead husband's armor, and they kiss just before Algren leaves.

When the Imperial Army confronts the samurai's rebel forces, the samurai fall back to higher ground, preventing the Imperials from using their superior firepower. As expected, Omura immediately orders the infantry, despite Bagley's misgivings, to pursue the samurai, sending the infantry straight into a trap. Setting fires to cut the enemy's immediate fighting strength in half, the samurai then unleash volleys of arrows on the infantrymen. Drawing their swords, the samurai, Algren and Katsumoto amongst them, charge the confused and wounded infantrymen. A second wave of Imperial infantry follows behind, as does the samurai cavalry, and a savage melee ensues that leaves many dead on both sides before the Imperial soldiers finally retreat.

Realizing that fresh Imperial forces are coming and that defeat is inevitable should a second battle occur, the surviving samurai resolve to make a final, fate-charged mounted assault. During the battle, Bagley shoots Katsumoto in the shoulder, but before he can finish off the samurai, Algren throws his sword at Bagley, killing him. On approaching the Imperial rear line and progressing far enough to scare Omura, the samurai are finally cut down by Gatling gun fire. Overcome by the sight of the dying samurai, an Imperial lieutenant originally trained by Algren orders the Gatling guns to cease fire against Omura's wishes. Katsumoto, observing bushido, asks Algren to assist him in performing seppuku; Algren obeys, ending Katsumoto's life. The Imperial troops show their still-lingering respect for the old order by bowing before the fallen samurai.

Later, as American ambassadors prepare to have the Emperor sign a treaty that would give the US exclusive rights to sell firearms to the Japanese government, Algren offers Katsumoto's sword as a present to the Emperor. The Emperor understands the message and tells the American ambassador that his treaty deal is not in the best interests of Japan. When Omura objects, the Emperor, realizing that he need not be ruled by Omura, confiscates his estates and fortunes. When Omura tries to protest, the Emperor then offers him Katsumoto's sword to commit seppuku if the dishonor is too great to bear. Omura merely lowers his head and walks away.

The movie ends with Algren - under a narrative provided by Simon Graham - returning to the samurai village and to Taka. Graham philosophically concludes Algren has found a measure of peace "that we all seek, and few of us ever find."

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