At the beginning of the story, hoping to learn more about the science to which he owes his human intelligence, Johnny is reading an encyclopedia article about chemistry.

Trotting over to the kitchen in hope of lunch, he finds the cook Honoria Velez in the same condition, and afterwards the station's scientists, including his patron Methuen, equally afflicted.

As part of an experiment of Bemis's, the balloons carry mold samples into the stratosphere to determine the mutational effects on them of cosmic rays.

Eavesdropping confirms this: it is one of the botanist's mutated molds, with will-inhibiting effects specific to higher anthropoids, that has afflicted the biological station.

After the conspirators part to attend to various errands, Johnny waylays and kills them separately, then breaks into Bemis's desk in search of the antidote he reasons they must have possessed.

Clumsily, with teeth and claws, he manages to open the bottle and fill one of the syringes, with which he trots back to the station in search of Methuen.

– which he plays to Methuen, forcing his mentor to pay attention to the message he had previously typed: "PICK UP SIRINGE AND INJECT SOLUTION INTO YOUR UPPER ARM."

A week later, beset by boredom in the now mostly-deserted biological station, Johnny attempts the chemistry article once more, still with no one available to help him through the difficult parts.

"The Command" is one of de Camp's earliest works of fiction, and, together with its successors "The Incorrigible," "The Emancipated" and "The Exalted," it represents his first effort to construct a connected series.

... [D]e Camp was capable of imagining what previously would have been thought of as lesser beings–[such as] a black bear experimentally raised to high intelligence in 'The Command' (Astounding, Oct. 1939) ... as being as decent, rational and civilized as most men manage to be, and maybe even more so.