A commercial airliner lands at JFK Airport in New York. A Secret Serviceman (Ken Scott), backed by a large Army contingent, greets the plane. After it taxis to a stop, Lieutenant Charles Grant USN (Stephen Boyd) steps out onto a mobile boarding ramp, verifies the Secret Service escort, and then signals to the other passenger, Jan Benes (Jean Del Val), to deplane with him. Benes walks down and gets into the Secret Service car, but not before warmly shaking Grant's hand one last time.
But as the motorcade enters a run-down section of New York, a car hurtles out of an alley and broadsides Benes' car. Hastily the Secret Service transfer Benes to another car, which then must make a quick escape as the Secret Service contingent fights a gun battle with several other assailants in the surrounding buildings.
Benes is taken to the underground headquarters of the Combined Miniature Deterrent Forces (CMDF) and given a full physical examination, including an EEG. The results are dire: he has suffered a stroke on the left side, in an inoperable spot. The doctors induce a coma so that his brain will not damage itself, while they decide what to do.
The original Secret Service man then picks up Grant and delivers him to an alley, instructing him to stay in the car and wait. Then the car, with Grant alone in it, descends to an underground complex. A small scooter bearing the CMDF logo, which he does not recognize, picks him up and delivers him to the Medical Section. There, Grant meets CMDF's commandant, Lieutenant General Alan Carter USA (Edmund O'Brien). General Carter first shows him Benes, in a coma and on a litter. Then he introduces him to the surgeon, Dr. Peter Duval (Arthur Kennedy), and his assistant Cora Peterson (Raquel Welch), who will operate on Benes, and also to Dr. "Mike" Michaels (Donald Pleasence), who is somehow expected to watch Duval to make sure that Duval does not try to kill his patient while operating. Then Carter explains what CMDF means, and about the miniaturization technique that is at the heart of it all. The problem: the USA (and the USSR) can miniaturize any object, to any size, but cannot hold an object miniaturized for more than 60 minutes. Benes knows how to extend the time, and Grant is the one who brought Benes out when he sought to defect. Now Carter reveals why Grant is there: CMDF will reduce a small submarine to microscopic size, and deliver Duval, Miss Peterson, Michaels--and Grant--into Benes' body, to operate on Benes from the inside.
Grant hates the idea. Worse yet, CMDF Medical Officer Col. Donald Reid (Arthur O'Connell) does not want a woman to go along on such a hazardous mission. Duval insists that he will have Cora or no one at his side. Grant also meets Captain Wilfrid Owens (William Redfield), designer and pilot of the submarine. The plan: reduce the submarine with all aboard and inject it into the left carotid artery. They will follow this to the site of the stroke, where Dr. Duval will use a hand-held laser to dissolve the clot. Then they travel back along the left internal jugular to the base of the neck, where they will be removed. The problem: if they stay in longer than 60 minutes, they will grow to a size that the immune system will notice, and Benes' own defenses will mobilize to destroy them.
Grant barely has time to take in a briefing before Michaels leads him, Duval, Cora, and Owens to a "sterilization room." There they dress in white SCUBA wetsuits, with white overalls over this, all bearing the CMDF logo, and pass through a corridor that irradiates them gently with UVA to kill any germs on their bodies. As Carter and Reid make their preparations, the crew then climbs aboard their submarine (USS Proteus, U-91035) and make preparations for getting under way. Owens and Grant install a tiny reactor containing a microscopic radioactive particle, that will power the sub once they are shrunk. (Radioactive material cannot miniaturize.) Grant tests the ship's wireless, which will be his station. Owens tells Michaels how he will be able to read Michaels' details charts of Benes' circulatory and lymphatic systems. Cora mounts and tests the laser, while also teasing Grant about his still-obvious fear of being "shrunk." (Grant has, throughout, tried to cover his fear with bad jokes and worse innuendo, and doesn't fool Cora for one second.) Cora also reveals that she is a five-year veteran of CMDF and has worked with Duval all that time.
Carter radios them to "prepare for miniaturization." So the crew pull out their seats, strap in, and settle in. Everything goes well, except for the time that Michaels, suffering an attack of claustrophobia, tries to get out through the topside hatch (after they are already submerged in an outsized hypodermic syringe), forcing Duval and Grant to restrain him and calm him down. (Duval and Grant have taken their first shot at working together, as they cooperate with Owens to accomplish the submersion.) With the second miniaturization step, the Proteus can now generate its own power. Eventually, the surgical team injects them into the carotid artery.
And then the problems begin. At first the view is fascinating, But then Proteus drifts into a strong current, then into a whirlpool. It catches the crew unaware, so that though Michaels and Duval can regain their seats, Grant and Cora cannot. Michaels' shoulder belts pop, and Duval struggles to hold him in. Cora is dragged into a bulkhead, and only Grant's iron grip on her stops her from breaking her neck. Finally the Proteus comes out of the whirlpool--but now the blood cells surrounding them are blue, not the red they remembered. They realize (as do Carter and Reid, watching from outside) that Proteus has gone through an arterio-venous fistula from the carotid artery into the jugular vein. Now they are headed toward the superior vena cava, and will go through the heart--which will smash them. Michaels urges immediate removal, but the authorities, under Carter's leadership, have another idea: to put Benes into cardiac arrest and let Proteus swim through as fast as her drive can propel her. This they do, and Proteus dives into the right ventricle and goes out through the pulmonic valve, with three seconds to spare.
Now they head into the lungs, where they observe oxygenation of the blue corpuscles that surround them. Just then, Proteus develops an air leak, which Owens stops, but only after Proteus has lost so much air that she cannot continue. Grant offers a solution: he will take the boat's snorkel and enter an alveolus to take the air that Benes breathes. Owens insists that everyone else aboard except himself join Grant in the dive, for safety reasons. As they put on their SCUBA gear, Grant discovers that the laser has broken loose and gotten knocked around. He firmly tells Duval and Cora to wait on testing the laser until after Grant finishes his snorkel operation.
Grant succeeds in pulling in the air--but then his safety line snaps and he finds himself sucked into a bronchiole with Benes' next breathe-out. When Benes breathes in again, he luckily finds the original alveolus, after which he races to safety, with Duval strenuously pulling him back out into the bloodstream.
Proteus gets back underway, heading into the pleural cavity. During this time, Cora disassembles the laser and discovers a smashed transistor and a broken trigger wire. Grant supplies replacements for both by cannibalizing the wireless and sending one last message, to the consternation of Carter and Reid. The transistor is of a good size, but the trigger wire is far too large--but Duval believes that he can scrape it down.
Grant also takes time to discuss with Michaels a hard reality: someone has tried to sabotage the mission at least twice. Grant knows that Cora had indeed fastened the laser securely--so someone must have unfastened it, just as someone tampered with Grant's safety line. Michaels protests that he cannot think so ill of Duval, the logical suspect.
Proteus enters the lymphatic system and passes through a lymph node. The boat blunders into several reticular fibers, and Owens warns that if they keep running into the seaweed-like fibers, they'll block the water jet intakes, and Proteus' engines will overheat. The crew also observe a stray bacterium, and antibodies attacking it and squeezing it to death.
Grant is frustrated with the delay and the slow progress. Duval then suggests going to the inner ear--a very hazardous path, because the slightest noise will kill them, and they cannot warn the operating team. Grant expresses confidence that the surgical team, once they see where they are headed, will keep the required silence. Michaels is still dubious, but reluctantly agrees to navigate to Benes' left ear.
Inside the ear, Owens must stop--the engines have overheated. Grant, Cora, and Michaels make another dive to pull the reticular fibers out of the intakes. Topside, a nurse (Shelby Grant) gets the idea of plugging Benes' ear with cotton--but then drops a pair of scissors to the floor. With the result that Proteus and her crew are badly shaken up. Cora gets the worst of it--she is carried into the Organ of Corti and finds herself trapped among the Cells of Hensen. She cries out for help, and Michaels and Grant race to her rescue--but Grant orders Michaels back aboard Proteus when he cannot go any further. Grant frees Cora from the hair cells, and they race back to the airlock--but as they wait for it to re-flood (after Michaels used it), antibodies attack Cora and fasten onto her. Grant hastily guides her into the airlock, closes the hatch--and then raps on the door when Cora makes plain that she simply cannot breathe. Michaels, Duval, and Owens open the airlock before it is fully evacuated, pull Cora out, and, with Grant's help, start pulling the antibody molecules off her body. Soon they start crystallizing and come off easily, so Cora is saved.
Proteus gets back under way, passes through the middle ear, and then passes through the endolymphatic duct back into the vascular system. Now they penetrate into the brain and reach the clot. During that passage, Michaels and Duval argue about whether Duval, having repaired the laser, should test it. Duval insists on using the laser as-is, not wanting to strain it.
Eventually they reach the clot. But with so little time remaining, Michaels wants Owens to take Proteus back out. But now Grant shuts down the power and insists that Duval and Cora go out and operate. Michaels strenously objects, but Grant firmly overrides him, saying that Duval simply does not fit the profile of a fanatic.
Now Grant makes his near-fatal mistake: instead of remaining aboard, he goes out to see if he can "help" Duval and Cora. Duval manages to clear the clot, at least enough to get the blood flowing again and relieve the pressure on a key nerve. But aboard Proteus, Michaels knocks out Owens, and then restores power, takes the helm, and sends Proteus on a collision course for the nerve. Grant asks for the laser, and fires a wide-angle beam at Proteus, raking her port side and sending her away from the nerve and into several nearby dendrites. White corpuscles respond immediately, so Grant slips back aboard, through the tear in the hull, to rescue Michaels and Owens if he can. Owens is only now regaining consciousness, so Grant tells him to suit up as fast as he can. But when he tries to untangle Michaels from the wrecked helm station, a white cell settles over the helmsman's dome, breaks through, and suffocates Michaels. Grant and Owens then abandon ship, before the white corpuscles crush it. Duval keeps the white cells at bay long enough for Grant and Owens to escape, before the laser quits for good.
Topside, Carter and Reid reluctantly order the removal of Proteus, because time has run out. Inside Benes' body, the four remaining crew swim as fast as they can along the optic nerve, toward Benes' left eye. Carter allows the attending surgeon to make preparations for a trephination procedure--and then deduces what the crew might do and stops the attending in mid-motion. Reid, too, realizes how they crew can still escape, and rushes down to the operating room and asks for a large magnifier. Through this, he looks into Benes' left eye, in time to make out four members of the crew swimming in Benes' tears. He calls for a microscope slide and uses it to lift out a teardrop, with the crew inside. Then he asks the staff to open the door, and as quickly as he dares, walks out into the miniaturization room and sets the slide gently down on the center hexagon. The crew then grows to full size, and the rest of the staff warmly greet them and assure them that the operation is a complete success.
NOTE: The film, as it played, had a number of scientific inaccuracies and plot holes. Isaac Asimov, who wrote the novelization from the final shooting script, repaired these and at least tried to produce a scientifically consistent narrative. The key differences are:
* The time limit on miniaturization is not a uniform sixty minutes. Instead, the rule is that energy of miniaturization (which is a function of the proportion of normal size to reduced size), when multiplied by duration of miniaturization, is equal to Planck's constant divided by two times pi. In simpler terms, the Heisenberg Uncertainty Principle governs the maximum time of miniaturization at any given size. Benes' secret is another set of variables that the original pioneering scientists overlooked. The sixty minutes that apply to this narrative are a special case of that model.
* Grant's role and authority are broader than as depicted in the film version. In the novel, Grant, not Michaels, has the ultimate authority on policy decisions, and is another brain and pair of hands in an emergency. Cora, sensing right away that the CMDF brass put him on board because they suspect Duval of murderous intent, at first resents him bitterly, and then softens toward him and almost pleads with him to understand Duval's politics, that have caused CMDF to doubt him. Those politics are that the Two Sides in the Cold War ought to share scientific discoveries freely, without regard to strategic sensitivity. But Duval *is not* the saboteur, a thing Grant comes to deduce by process of elimination.
* When Grant makes his first dive with the snorkel into Benes' lungs, Owens uses the on-board miniaturizer that Proteus carries, to reduce the air to a size compatible with Proteus and her crew in their shrunken state. Otherwise, Grant would have been trying to draw in oxygen molecules large enough to see.
* When Grant's safety line parts, sending him up the bronchiolar tree, Duval suggests that Owens orient the Proteus to face the alveolar wall and shine the boat's headlight into it. That allows Grant to find the right alveolus again. Otherwise he would have been hopelessly lost.
* As Carter and Reid watch Proteus enter the inner ear, they do not use their PA system to announce to the surgical team the hazard against making noise. Instead, Carter writes a note and sends an orderly to walk into the OR in his stockinged feet to hand it to the attending. When, later, he wants to suggest plugging Benes' ears, he sends another note the same way. (The nurse does not take that upon herself, but acts only when she gets Carter's second note. And when the scissors fall, she steps on them so that they won't rattle and thus risk more damage than they might already have caused.)
* When Cora falls into the organ of Corti and finds herself wedged among the hair cells, the antibodies take time to "taste" her before they come swarming. Benes' body would never have had antibodies specific to her at the moment of contact. This is still a stretch, because the immune system is now known to take much longer than that to raise antibodies to anything, and through a process that is much more complex than that depicted in film or novel.
* When the crew pull Cora back aboard, they only have to give one good tug at one clinging antibody molecule, before realizing that all the antibodies crystallize at once, and all they need do is brush them off. The air on board "hits" the antibodies and denatures them immediately. So the dramatic (and suggestive) grabbing procedure is not necessary.
* When Duval and Cora make their dive to attack the clot with the laser, Cora wears her wetsuit inside out, in order not to present a recognizable target to any stray antibodies that might be lurking about. Benes might not have been "immunized" against her before, but he is now.
* After clubbing Owens, Michaels, unaccountably, bundles him into a wet suit and drops him out the airlock. Perhaps Michaels takes no chances that Owens might come to himself and try to take his ship back. With the result that Grant's quick rescue operation becomes unnecessary.
* After the Proteus crashes into the dendrites, Duval worries that the damage that Michaels has done might start a new clot. This apparently does not happen, but at least Asimov acknowledges the possibility, which the original script does not even talk about.
* After the white corpuscles eat the Proteus, Grant knows that they can't just leave her in place. Even when crushed, Proteus will grow to a size to kill Benes. (Michaels also realizes this at the last instant of his life, which is why he bursts out laughing as the white corpuscle collapses the glass dome over his head.) So Grant takes out his dagger and slashes at the white cell to attract its attention and induce it to follow them out. Of course, that releases chemotaxins that bring a swarm of white cells, so the crew must swim for their lives to get out ahead of them. (Furthermore, the medical team topside do not stop tracking Proteus even as they prepare for the trephination procedure. When the monitoring techs realize that Proteus seems to be moving again, Carter stops the preparations. That's when Reid realizes that the crew are using an escape route he did not at first consider.)
* The crew, swimming toward the eye, do not drop the laser. Instead, Cora tries to carry the laser out. When Cora inevitably starts flagging, Grant takes the laser and its power pack away from her so that she can swim unencumbered.
* Finally, when Col. Reid extracts the crew, he does not try to walk with the slide into the miniaturizer room. Instead, he sets the slide on the operating-room floor where he stands and orders everyone out of the room, including Benes, whom the staff wheel out on his litter. When the crew re-magnify, General Carter takes a quick muster with his eyes and realizes, with a sickening feeling in his gut, that Michaels and the Proteus are both missing. Grant stops him and assures him that the pile of metal fragments next to the crew is what's left of both.
The novel has a few more dramatic differences--offering a more detailed explanation of the science of miniaturization, and making more of the professional (or personal) relationships between General Carter and Colonel Reid, between Reid and Michaels, between Grant and Benes on the flight in, between Duval and Cora, and especially between Cora and Grant during and after the trip. (See above.) Grant also has a scene with Carter and Reid in which he acknowledges his mistake in going out on the dive with Duval and Cora, instead of remaining on board after he, in effect, had placed Michaels under arrest. The novel ends with an inspiring scene in which Grant, fully grown once more, pays a visit to Benes, who by now has regained consciousness and can even talk to him.
BENES: And now I must remember what I came here to tell. It's a little fuzzy, but it's still all in there.
GRANT: You'd be surprised to know what's in you, Professor.