Harry Kilmer (played by Robert Mitchum) is a veteran Marine and one time private eye, whose friend George Tanner (Brian Keith) is in trouble - his daughter and her boyfriend are missing; Tanner is in business with the dreaded Japanese yakuza or mafia. He has been arm twisted by Tono (played by Eiji Okada) who has taken the girl and her friend captive, just so that George will go through a shady business deal involving the sale of illegal arms. Since Tanner and Kilmer have been friends for long, having served in Tokyo post the War, the former hopes that the detective’s connections in Japan will help rescue his daughter.
Years ago, Harry had fallen in love with a Japanese lady by the name of Eiko (played by Keiko Kishi), in fact he had helped keep her daughter alive by getting the child much needed penicillin. They were inseparable, even living together, until Ken, her brother who was in the Imperial army returns home. He is livid that Eiko should have an affair with the enemy, however, his principles dictate that he be indebted to Harry for having saved his niece - this would mean that at any time, then or even years later - he would be obliged to repay the debt if Kilmer decided.
Harry had proposed marriage to Eiko but she turned him down – she was not likely to bring more dishonor to her brother and family. As a parting gift, Kilmer borrows five thousand dollars and buys a bar for Eiko, which she converts to a coffeehouse. The two know each that their feelings for each other are so strong that none would find another love - and now, when Harry returns to Tokyo after years - his first stop is the coffeehouse. Meanwhile, Ken joins the feared yakuza - he has no contact with his sister now, and does not speak to her.
He once more proposes to Eiko, who, although she still loves him, also still considers the honor of her family to be a priority. Citing the debt, she tells Harry to meet Ken in Kyoto. When he travels to meet Ken along with Tanner’s bodyguard Dusty (played by Richard Jordan), Ken tells him that he is no longer with the yakuza but he knows enough to be able to be of help. The sense of obligation he has bids him to take up arms once more, and he partners with Harry to rescue George Tanner’s daughter and her friend.
In combat, Ken injures one of Tono’s underlings, and his cover is blown - because the leader sees his involvement as an unnecessary interference. Tono orders the death of both men. On the other hand, Eiko suggests that Harry speak to Goro (played by James Shigeta), to intercede on the men’s behalf; however, he refuses as he is neutral to the affairs of the yakuza. Kilmer is left with no alternative, but to plan Tono’s death. Harry sees himself as the reason for causing such grief and anguish in Eiko’s life again, and endangering Ken’s life - he is guilt ridden and decides to stay back in Tokyo, although he imhas completed the favor George Tanner had wanted of him.
The story gets a fresh twist after a failed attempt on his life, Harry discovers that money-ties are thicker than bonds of friendship, and that Tanner is the one who has sided with Tono, to kill his one time friend and confidante. Shattered, though not surprised, he begins to plan his next move. In a gun battle meant to kill him and Ken, Eiko’s daughter is shot dead, whilst Dusty is killed with a sword. Both Ken and Kilmer, and Eiko are plunged into grief.
Goro steps in to help the two men, making use of his son, who is part of Tono’s yakuza. However, he seeks the favor that his son be spared his life. The boy has a defining spider tattooed on his head. Another shocking revelation is in store for Harry, as Goro discloses to him that Ken is not Eiko’s brother, but her husband! Hanako was their only child - a stunned Harry understands the anguish his presence has caused in the lives of the two people he has come to love and respect. Kilmer hunts down Tanner and kills him, whilst Ken takes Tono’s life with a traditional katana. Goro’s son attacks them and is killed in self defense - as Ken thinks of ending his own life for not having been able to keep his word to Goro - the man stops him. As a peace offering and an apology, Ken cuts off his little finger.
Before leaving Japan, Kilmer pays a visit to Ken, and whilst the latter goes in to prepare a cup of tea for him, Harry commits yubitsume - cutting his little finger and placing it in a handkerchief for Ken. He seeks the man’s forgiveness, asking him to also forgive Eiko. The two part but not before Ken remarks “no man has a greater friend than Kilmer-san.”