The show opens in Japan, as a picture of Mount Fuji with "Japan" superimposed on it tells us. Two men who we will later discover to be assassins are praying in a temple.
The next scene is in "Hawaii" (another superimposition over the Aloha Tower). Leonard Tokura (Ricardo Montalban) arrives in his Rolls-Royce for a court hearing. A reporter for TV station KGMB (Bob Sevey) asks Tokura what does he think about the Attorney General's charge that he is head of organized crime in Hawaii. Tokura brushes this off, saying that he is "the head of Tokura Imports, a legitimate business."
Suddenly, one of the two assassins we saw in the opening scene rushes through the crowd and shoots Tokura point-blank. The killer is himself shot dead by Tokura's men. Tokura drops to the floor, but because he is wearing a bulletproof vest, he gets up and continues into the courtroom, saying "I mustn't keep the Crime Commission waiting."
The man asking Tokura questions in court is the Hawaiian Attorney General Walter Stewart (Morgan White) himself. But after the first thing that Stewart "propounds," Tokura invokes the Fifth Amendment against self-incrimination.
McGarrett has a "surprise witness" in the form of Mary Travers (Karen Norris), a former bookkeeper at Tokura's company, ready to testify, but Danno says there is something wrong with her: "She was fine all morning, till about a half an hour ago." Mary tells the two of them that she is ready to go on the stand. When Stewart starts asking her questions about "a set of books, secret books, which revealed your employer's interest in such things as narcotics, prostitution... [at this point Stewart is told to stop leading the witness]," Mary, who has become more and more agitated, drops dead.
At the Five-O offices the next day, McGarrett tears a strip off Danno, telling him, "It was your job to protect her, to keep her alive. Your job. I put you in charge." Danno yells back at his boss, "You want me to say I blew it? All right, I blew it, I blew it. Look, Steve, I was with her every second. When I wasn't there, Chin Ho or Kono was. Nothing, nobody got close to her. The food she ate, one of us tasted it first. If she wanted a candy bar out of a machine, I took the first bite."
Details about Tokura's assassin are sketchy. Chin Ho produces the gun that was used and also what looks like a Japanese ceremonial knife.
Tokura, who was born in San Francisco, has lived in Hawaii for years, currently with his jet-setting daughter Deedee (Carolyn Barrett). After a meeting with the Governor, McGarrett goes to see Tokura and shows him the knife, saying "Samurai, ancient order of Japanese knighthood, fanatic principles of honor. The code of Bushido." (This is the beginning of misuse of the term "bushido" in the show; see the review below.) McGarrett offers to provide Tokura with protection against future assassination attempts, but Tokura just brushes this off. When Deedee shows up, there is a certain attraction between her and McGarrett and Tokura wonders if McGarrett has "pressing affairs elsewhere." McGarrett leaves.
McGarrett and Danno visit the medical examiner's office where the resident doctor (Newell Tarrant) tells them that Mary Travers was killed by some "procnine" (a bogus poison) in her lipstick.
Tokura and Deedee go to an engagement. The second assassin is waiting for them there. He runs toward Tokura, clutching a grenade, but one of Tokura's bodyguards grabs him as the grenade explodes, presumably killing them both.
Shortly after this, Deedee tells her father to contact McGarrett, who soon shows up at their place. Deedee tells McGarrett if he doesn't provide protection she will shoot her father herself and end the waiting. Her father keeps telling her to be quiet. McGarrett thanks Tokura for predicting how Mary killed herself when he suggested she was poisoned during McGarrett's previous visit. Deedee tells McGarrett that if he wants to arrest her father, he will have to keep him alive.
When Deedee leaves, McGarrett grills Tokura, who says that he has no idea why someone in Japan wants him dead, and that he has never been in Japan. Tokura runs through his history in Hawaii, including being forced into an internment camp after Pearl Harbor because he was "a Jap." He escaped and went to Molokai, where he stayed in a cave until the end of the war. After this, McGarrett says, he started Tokura Imports which had business in "refugees, women, drugs and gambling." Tokura tells him "You never give up, do you?"
Just at this moment, someone with a long-range rifle takes a shot at Tokura from the boundary of his property. McGarrett and Tokura's bodyguards start shooting back at him. Suddenly, Tokura yells for help as two more men grab him. They shoot at McGarrett. When McGarrett comes back to where he was talking to Tokura, he finds Tokura's body with the face blown off. Deedee appears and freaks out.
As Tokura's body is taken away, his ring slips off his finger, which makes McGarrett suspicious because when he was alive, his ring fit so tight he couldn't even twist it. "Tokura dead, they move the body and it slides off."
Tokura's mug shots and fingerprints are telephotoed to Tokyo police, who report back that the prints match "S. Yamashito, lieutenant, Imperial Navy. Served on board kamikaze submarine, Pearl Harbor, 1942. Killed in action."
McGarrett goes to see a friend of his at the local Navy base who is a Chief Petty Officer (Ed Sheehan). His friend remembers that a couple of years ago, a two-man Japanese submarine like this was discovered off Molokai and there was the remains of one body still inside.
Armed with this information, McGarrett goes to see Deedee. He tells her that he thinks that her father is still alive, that he was a Japanese naval officer, and the body in their house was someone else's. McGarrett continues, telling her that her father met someone named Tokura hiding from Japanese internment in a cave on Molokai and assumed his identity.
Deedee tells McGarrett that his theory is "sick." She says "My father loved me," but McGarrett replies, "Sure he did. But he loved himself more." Deedee says "whatever" (twice). But when McGarrett then asks her "Would you bet a million dollars that I'm wrong about your father?" She says "Yes, Mr. McGarrett, yes."
McGarrett convinces Deedee to motivate her father to come out of hiding by giving a million dollars in his memory to the local university. Shortly after this, she appears on TV making such a donation.
Not surprisingly, Tokura contacts her soon and the two of them meet in a Japanese movie theater. Tokura tells his daughter that her gift to the college was "foolish" and he wants her to cancel the check. Then he wants her to buy a ticket to Geneva where he will eventually meet her. Deedee is disturbed by her father's deception, but not as much as Tokura is when he realizes that McGarrett has used his daughter to lay a trap for him. HPD cops are in the theater and take Tokura into custody.
At the docks, Tokura is going to be deported. The only charge which they can make stick against him is that of "illegal entry," and two immigration officials are present to make sure he gets on a boat. But there are two suspicious guys at the top of the gangplank which cause Tokura to hesitate boarding since he thinks they are "bushido." He pleads with McGarrett not to make him leave, saying he will give him "anything you want. The books, the entire operation." When McGarrett says no dice, Tokura finally admits that he killed Mary Travers. The two men from the boat, who are actually HPD cops, arrest Tokura and he is taken away.
Kono tells McGarrett "Beautiful snooker." Danno adds "Remind me never to bet against you." McGarrett ends the show by saying "Confession is good for the soul."