Johnny Got His Gun takes a harrowing look inside the mind of a World War I draftee who is lying helpless without arms, legs, mouth, ears, nose, or eyes, yet over the course of years is determined to reestablish contact with the outside world and tell "little guys" never to allow bellicose politicians to butcher them again.

World War I draftee Joe Bonham is lying in a hospital, bandaged all over and realizing he is at least deaf and has lost both arms. The discovery process is slow, as he weaves in and out of consciousness, remembering the family and girlfriend he reluctantly leaves behind. Bonham knows he has not come to make the world safe for democracy. He remembers saying farewell to beautiful nineteen-year-old Kareen Birkman after making love with her the night before the troop train arrives. She begs him not to report. Their farewell takes place against a mish-mash of patriotic songs, speeches, and prayers, by which point the lovers have no time for prayer.

Through flashbacks, Bonham recalls a failed high school romance and a one-day escape from reality into the Utah desert, contemplates friendship and betrayal and the antics of an amusing fellow in the bakery where he works in Los Angeles. Bonham emerges from his flashback only to realize that they are far more extensive and he is being kept alive against his will, unable to protest. He has one sense left: feeling on the remaining parts of his body. Bonham despises the medical profession, which has profited from the war, learning techniques that culminate in saving him when they should have let him go.

Bonham feels a rat gnawing persistently at an unhealed side wound and only when his nurse is tending him does he realize the rat is a dream. He decides he must be able to discern reality from dream, for that is all he has left. Bonham realizes even if loved ones were beside him, he would not know. This leads him to think about those who enlist "little guys" into fighting wars over ideals. Bonham claims bona fides as the only living dead man in history and the sole right to speak for the dead. All patriots and idealists are liars and frauds.

Trying to keep his mind busy, Bonham laments having wasted his school years. He determines he must conquer time, but his early attempts are too complex. Eventually, he simplifies his methods; they work, and he declares that day New Year's. He resents receiving a medal and but wants the "big guys" to see what they have done for him. Receiving the medal, Bonham realizes that if vibrations can communicate to him, he should be able to communicate by them. He begins continually tapping SOS in Morse code with his head against his pillow, but soon despairs that his day nurse will ever understand. He wants to die, for this alone will give him peace. Bonham feels certain that a doctor will understand his tapping, but instead is merely tranquilized. In a dream, Bonham sees Christ playing cards with draftees soon to be dead, and falls weeping at his feet.

Bonham receives a temporary day nurse who traces "Merry Christmas" on his chest. This communication brings elation and he resumes his SOS, but the doctor whom she summons rejects Bonham's wild ideas of becoming a sideshow freak to earn his own way in the outside world (while demonstrating the hidden horrors of war). Drugged again, he sees himself as a new messiah and formulates a platform: the little guys who, throughout history, have obeyed the big guys, fought, and died, will never again permit this to happen. Every Johnny handed a gun will know where to point it.