Captain Kirk, Mr. Spock and Lt. Uhura (whose name is misspelled "Uhuru" throughout the entire comic) take a shuttlecraft to the surface of an unknown planet in sector 199-D, in order to investigate intelligent radio signals received from the area. They discover a highly advanced city and land in the middle of it, but the city is deserted. The landing party moves on to a nearby town (smaller than the first), and finds it empty also. They set out to explore more of the planet, and discover another city less than a mile away from the first two. It is a miniature city! The buildings and trees are only waist-high and abandoned vehicles are scattered about. (Including several classic cars in the 50's style, complete with tail fins!) That city, too, is abandoned. "A midget city!" exclaims Uhura. "Could there have been two races here of different sizes?". "And both abandoned" Kirk continues, "All intelligent life gone? What about the radio signals?". In order to explore more territory, Kirk orders Mr. Spock and Uhura to follow another path. They agree to meet again in three hours.
As Kirk explores the area, a miniature craft flies past him, and lands behind a nearby hill. He quickly moves to investigate. "A toy rocket!" he exclaims, finding the vehicle parked on the ground. "Amazingly detailed! Still warm, too! Then the child who flew it must be nearby!". He picks the craft up to examine it, but it suddenly flies away, and he is unable to hold on to it. Several minutes after the first ship disappears, a large group of small ships arrives. The miniature ships begin firing weighted wires at Kirk. Soon, he is hopelessly entangled on the ground, unable to move. One of the ships lands, and a group of tiny soldiers emerges!
"Allow me to explain" Madame President begins. "My people are all three civilizations you have seen! Once we were as tall as you! We were a happy world until sudden explosions rocked our sun with fantastic intensity! But in time, these ceased and life resumed as before!". However, the people of her world soon discovered that they were shrinking with each passing day. "Investigations were swiftly ordered" Madame President continues, "but still the strange shrinking continued!
Uhura suggests using the Enterprise to transport the inhabitants of Kujal away from the planet, but Madame President refuses, citing her people's love of their homeworld. Kirk offers his help to resolve the situation, and Madame President takes time to think about it. Meanwhile, she allows the Enterprise crew to meet with each other. "Obviously the only hope lies in understanding the strange new waves that emanate from that sun and building some antidote or defense" Kirk says. "I propose that we fly close to their sun and gather as many samples of its rays as possible!". "And have you thought what those rays might do to us?" Uhura replies. "Probably shrink our cells as it did theirs" Kirk answers. "And the closer we get, the faster the process!". Madame President and General Kwy have been listening in, and they agree to the plan. Kwy demands that a hostage be left behind, so that Kirk and the others don't simply try to escape.
The Enterprise approaches the sun of the planet Kujal, using special "anti-radio wave" shielding to protect itself against the harmful rays. Sulu attempts to raise the radio energy analyzer dish, but it jams. Scotty volunteers to go outside and repair it, wearing a special protective suit. "Dinna worry" he tells Kirk, "The foil will protect me!". Scotty is able to free the jammed dish, but collapses outside the ship as soon as he is finished. "Break out another foil outer gear!" Kirk tells Spock. "I'm going after him!". Kirk exits the ship, and finds that Scotty's suit is empty! Later, as Spock and McCoy examine the suit with him, they discover Scotty inside, shrunken down just as small as the people on Kujal! Kirk finds a rip in the fabric of Scotty's suit. "Here's the answer" he says. "The edge of the dish tore this tiny hole in your foil gear and the shrinking rays poured through!"
At that moment, in the microscopic world that Scotty has entered, he ponders his situation. "Then here I am" he thinks, "Smaller than a salt grain with nothing else as far as my eyes can see, which is probably an inch!". Just then, a monstrous germ appears, and tries to eat him! Scotty runs away, narrowly avoiding huge rocks falling from above. "Boulders!" he thinks, "Bits of microscopic dirt of course! But big enough to kill me! Some sealed system!". Scotty uses the rocks to attack and kill the germ. Then, a huge pole lifts him up off the ground and carries him into the air!
In the world of "giants", McCoy looks at the microscopic Scotty, who is on the end of a needle! "Are you sure you've got him Doctor?" Spock asks. "Yes" replies McCoy, "I can see him clearly through these micro-specs! He's struggling like a demon!". Spock places the microscopic Scotty on a glass slide, and fires an experimental "anti-shrink ray" at him. Within seconds, Scotty begins to grow large again! "Listen" says Spock, straining to hear. "He's trying to tell us something!". "The first report by a human returned from the land of microbes!" Kirk adds. Scotty is less than amused by his situation, as he grows larger. "Get me some clothes, mon!" he shouts, "I'm poppin outta this silly thing!".
Later on the Enterprise, Scotty discusses events with Kirk and Spock. "And I'll tell you one thing" he says to them, "I'll never make fun of another man's size again!". "Experience is a great teacher!" says Spock. "Teacher?" Kirk answers, "This kind of experience is a full professor!".