An American spacecraft is hijacked from orbit by another, unidentified spacecraft. The U.S. suspect it to be the Soviets, but the British suspect Japanese involvement since the spacecraft landed in the Sea of Japan. To investigate, MI6 operative James Bond—agent 007—is sent to Tokyo after faking his own death in Hong Kong and being buried at sea from HMS Tenby (F65).
Upon his arrival, Bond is contacted by Aki, assistant to the Japanese secret service leader Tiger Tanaka. Aki introduces Bond to local MI6 operative Dikko Henderson. Henderson claims to have critical evidence about the rogue craft but is killed before he can elaborate. Bond chases and kills the assailant, disguises himself and escapes in the getaway car, which takes him to Osato Chemicals. Once there, Bond subdues the driver and breaks into the office safe of president Mr. Osato. After stealing documents, Bond is chased out by armed security, eventually being picked up by Aki, who flees to a secluded subway station. Bond chases her, but falls down a trap door leading to Tanaka's office. 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.
Bond goes to Osato Chemicals to meet Mr. Osato himself, masquerading as a potential new buyer. Osato humours Bond but, after their meeting, orders his secretary, Helga Brandt, to have him killed. Outside the building, assassins open fire on Bond before Aki rescues him. The assassins are disposed of via a helicopter with a magnetic grab. Bond and Aki continue driving to Kobe, where the Ning-Po is docked. Bond and Aki investigate the company's dock facilities and discover that the ship was delivering elements for rocket fuel. After being discovered by more henchmen, they give chase but Bond eludes them until Aki gets away; however, Bond is captured and knocked out. He wakes, tied up in Helga Brandt's cabin on the Ning-Po. She interrogates Bond, who bribes his way out of imprisonment. Brandt then flies Bond to Tokyo, but, en route, she sets off a flare in the plane and bails out. Bond manages to land the crashing plane and escapes.
After finding out where the Ning-Po unloaded, Bond investigates the area by a heavily armed autogyro, Little Nellie, delivered to him by Q. Near a volcano, Bond is attacked by helicopters, which he defeats, confirming his suspicions that the enemy's base is nearby. A Soviet spacecraft is then captured by the unidentified craft, heightening tensions between Russia and the US. After capturing the Soviet spacecraft the ship lands in an elaborate base on the inside of a volcano. It is revealed that the true mastermind behind this is Ernst Stavro Blofeld and SPECTRE. Blofeld seems to forgive Brandt for her failure to kill Bond, but as she leaves, he activates a collapsing section of walkway under her, dropping her into a pool of piranha. Blofeld demands that Mr. Osato kill Bond.
Bond prepares to conduct a closer investigation of the island by training with Tanaka's ninjas, during which an attempted assassination on Bond kills Aki. Bond is disguised and stages a marriage to Tanaka's student, Kissy Suzuki. Acting on a lead from Suzuki, the pair sets out on reconnaissance to the cave, investigating the cave and the volcano above it. Establishing that the mouth of the volcano is a disguised hatch to a secret rocket base, Bond slips in through the crater door, while Kissy returns to alert Tanaka. Bond locates and frees the captured astronauts and, with their help, steals a spacesuit in attempt to infiltrate the SPECTRE spacecraft "Bird One". Before he can enter the craft, Blofeld notices Bond, and he is detained while Bird One is launched.
Bird One closes in on the American space capsule and US forces prepare to launch a nuclear attack on the USSR. Meanwhile, the Japanese Secret Service ninjas climb the mountain and attempt to enter through the upper hatch, but are spotted by the base's security and fired upon. Bond tricks Blofeld and manages to create a diversion that allows him to open the hatch, letting in the ninjas. During the battle, the control room is evacuated and Osato is killed by Blofeld. Bond escapes and fights his way to the control room via Blofeld's office, where he defeats Blofeld's bodyguard, Hans, dropping him into the pool of piranha. Bond activates the spacecraft's self-destruct before it reaches the American craft and the Americans stand down their weapons.
Blofeld activates the base's self-destruct system and escapes. Bond, Kissy, Tanaka, and the surviving ninjas escape through the cave tunnel before it explodes, and are rescued by submarine.