The United States and the Soviet Union have both developed technology that can miniaturize matter by shrinking individual atoms, but only for one hour.

A scientist. Dr. Jan Benes, working behind the Iron Curtain, has figured out how to make the process work indefinitely. With the help of American intelligence agents, including agent Charles Grant, he escapes to the West and arrives in New York City, but an attempted assassination leaves him comatose with a blood clot in his brain that no surgery can remove from the outside.

To save his life, Grant, Navy pilot Captain Bill Owens, medical chief and circulatory specialist Dr. Michaels, surgeon Dr. Peter Duval, and his assistant Cora Peterson are placed aboard a Navy ichthyology submarine at the Combined Miniature Deterrent Forces facilities. The submarine, named Proteus, is then miniaturized to “about the size of a microbe”, and injected into Benes’ body. The team has 60 minutes to get to and remove the clot; after this, Proteus and its crew will begin reverting to their normal size, become vulnerable to Benes’s immune system, and kill Benes.

The crew faces many obstacles during the mission. An undetected arteriovenous fistula forces them to detour through the heart, where cardiac arrest must be induced to, at best, reduce turbulence that would be strong enough to destroy Proteus. As the crew faces an unexplained loss of oxygen and must replenish their supply in the lungs, Grant finds the surgical laser needed to destroy the clot was damaged from the turbulence in the heart, as it was not fastened down as it had been before: this and his safety line snapping loose while the crew was refilling their air supply has Grant begin to suspect a saboteur is on the mission. The crew must cannibalize their wireless radio to repair the laser, cutting off all communication and guidance from the outside, although because the submarine is nuclear-powered, surgeons and technicians outside Benes’s body are still able to track their movements via a radioactive tracer, allowing General Alan Carter and Colonel Donald Reid, the officers in charge of CMDF, to figure out the crew’s strategies as they make their way through the body. The crew is then forced to pass through the inner ear, requiring all outside personnel to make no noise to prevent destructive shocks, but while the crew is removing reticular fibers clogging the submarine’s vents and making the engines overheat, a fallen surgical tool causes the crew to be thrown about and Peterson is nearly killed by antibodies, but they are able to reboard the submarine in time. By the time they finally reach the clot, the crew has only six minutes remaining to operate and then exit the body.

Before the mission, Grant had been briefed that Duval was the prime suspect as a potential surgical assassin, but as the mission progresses, he instead begins to suspect Michaels. During the surgery, Dr. Michaels knocks out Owens and takes control of Proteus while the rest of the crew is outside for the operation. As Duval finishes removing the clot with the laser, Michaels tries to crash the submarine into the same area of Benes’ brain to kill him. Grant fires the laser at the ship, causing it to veer away and crash, and Michaels to get trapped in the wreckage with the controls pinning him to the seat, which attracts the attention of white blood cells. While Grant saves Owens from the Proteus, Michaels is killed when a white blood cell consumes the ship. The remaining crew quickly swim to one of Benes’ eyes and escape through a tear duct seconds before returning to normal size.