Ben and Leslie Cash live largely off the grid with their offspring -- Bodevan, Kielyr, Vespyr, Rellian, Zaja and Nai -- in a cabin in the mountains of Washington state. The parents have passed their socialist and survivalist ideals to their children. Ben considers most of Western society to be fascist, especially corporate America. He also believes that no one will or should be there for you, so you'd better learn how to take care of yourself. As such, the children have been subject to vigorous physical training; know how to deal with minor bumps, bruises, cuts, sprains, and even fractures; and know how to hunt, forage, and grow their own food. The children are also non-registered home schooled, meaning that they have no official academic records. Ben and Leslie have tried to make the children critical thinkers, however, within the context of their ideals. Beyond these issues, Ben and Leslie made the decision to live this lifestyle for Leslie's health. Formerly an attorney, Leslie was diagnosed as bipolar. Ben believes that this disorder started with her postpartum depression with Bo. Yet Leslie's condition has worsened. Despite not believing in Western medicine, Ben sends Leslie to a hospital close to Ben's sister, Harper, so that there can be family close by. While hospitalized, Leslie commits suicide. Beyond the collective grief, Leslie's act brings out a battle between Ben and Leslie's father, Jack Bertrang, a Christian who not only blames Ben for Leslie's death, but believes that what he is doing "to" the children can legally be considered abuse. Jack takes over the funeral arrangements as per his and his complacent wife Abby's Christian morals, against what Ben knows was Leslie's wishes, as she believed in Buddhist philosophies. Although Jack threatens to call the police if Ben shows up to the funeral, Ben and the children believe it is their mission to honor Leslie's last wishes to be cremated as per Buddhist philosophy. This mission not only may bring the divide between Jack and Ben to a head, but may also bring out some long dormant issues between the Cash children as they are exposed to commercial America in all its good and bad, and as Bo grows into manhood, he may have his own ideas of what he should do with the next phase of his life.

In the 1870s, Captain Nathan Algren (Tom Cruise), a cynical veteran of the American Civil War, who will work for anyone, is hired by Americans who want lucrative contracts with the Emperor of Japan to train the peasant conscripts for the first standing Imperial Army in modern warfare using firearms. The Imperial Omura (Masato Harada) cabinet's first priority is to repress a rebellion of traditionalist Samurai, hereditary warriors, who remain devoted to the sacred dynasty, but reject the Westernizing policy, and even refuse firearms. Yet, when his ill-prepared superior force sets out too soon, their panic allows the sword-wielding samurai to crush them. Badly wounded, Algren's courageous stand makes the samurai leader Katsumoto (Ken Watanabe) spare his life. Once nursed to health, he learns to know and respect the old Japanese way, and participates as advisor in Katsumoto's failed attempt to save the Bushido tradition, but Omura gets repressive laws enacted. He must now choose to honor his loyalty to one of the embittered sides when the conflict returns to the battlefield.

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