Jupiter 16, a U.S. space capsule, is orbiting the Earth when another spacecraft approaches and swallows it up, severing one astronaut's lifeline and leaving him to die in space. The United States believes the Soviets are behind the heist, but the British suspect Japanese involvement since the spacecraft disappeared somewhere in the Sea of Japan.

In Hong Kong, 007 is enjoying a romantic encounter with a Chinese woman who leaves Bond in a pull down bed and pushes a button that lifts it, trapping him in the wall. Two men then burst into the room with machine guns and spray the upright bed. When the police arrive, the woman has disappeared and Bond is found dead.

The film's producer wanted his friend Frank Sinatra to perform the song, but Frank suggested they use his daughter Nancy, who was enjoying great popularity in the wake of her single, "These Boots Are Made for Walkin'". You Only Live Twice has become one of Nancy Sinatra's best known hits.

Bond is buried at sea from HMS Tenby. As soon as his casket hits the sea floor, it is retrieved by MI6 agents and taken aboard a submerged submarine, whereupon the casket is opened and a healthy Bond emerges. His assassination in Hong Kong was a ruse to trick his enemies into believing he was dead so he can continue his mission undetected.

When 007 is ordered to Japan to meet with members of Japan's SIS, Miss Moneypenny helpfully tosses him a copy of Instant Japanese, but Bond tosses it back, saying, "You forget, I took a first in Oriental languages at Cambridge."

Upon his arrival, Bond attends a sumo match where he is approached by Japanese secret service agent Aki, who takes him to meet local MI6 operative Dikko Henderson.

He lost his leg in Singapore in 1942, serving in the British Army during WWII. Henderson claims to have critical evidence about the rogue spacecraft, but is killed before he can elaborate.

After obtaining secret documents, Bond is pursued by armed security, but is rescued by Aki, who flees to a secluded subway station. Bond chases her, but falls down a trap door leading to the office of the head of the Japanese secret service, Tiger Tanaka. The stolen documents are examined, and found to include a photograph of the cargo ship Ning-Po, with a microdot message saying the tourist who took the photo was killed as a security precaution.

TANAKA: Do you like Japanese sake, Mr. Bond? Or would you prefer vodka martini?
BOND: Oh no. I like sake. Especially when it's served at the correct temperature. 98.4 degrees Fahrenheit like this is.
TANAKA: For a European, you are exceptionally cultivated.

Posing as Mr. Fisher from the British company Empire Chemicals, Bond pretends to be interested in a contract with Osato Chemicals. He is warmly greeted by Mr. Osato and Helga Brandt, his glamorous henchwoman and SPECTRE No. 11. However, Osato knows the truth and orders his men to kill Bond.