Machinal begins in an office setting with a small staff completing their duties. Enter Young Woman, the protagonist. She is late and seems distracted, and her coworkers tell her that she will soon be fired if she cannot get herself together. The Telephone Girl says that Mr. J, the boss, wants to see the Young Woman in his office. While she is out of the room, the staff gossips over whether or not the boss will ask her to marry him and whether or not she will accept. Their suspicions are confirmed when the Young Woman reenters seeming worried and confused. They each offer different bits of advice, and the stage goes black at the end of the Young Woman's disjointed speech on her fears of marrying Mr. George H. Jones.
Episode Two opens in the Young Woman's kitchen. As she and her Mother are cleaning up after dinner, the Young Woman blurts out that there is a man who wants to marry her. Her mother seems skeptical at first, but quickly changes her mind once she learns that Mr. Jones is the Vice-President of his company. The Young Woman argues that she does not love him; she longs for someone young with wavy hair rather than Mr. Jones with his bald head and fat hands. This argument continues up until the last lines of the episode when the Young Woman decides that she will marry him, because she feels obligated to.
There is a small skip in time, and by Episode Three, the new couple has arrived at their lavish honeymoon suite. The Young Woman is extremely uncomfortable and keeps looking out the window, searching for a glimpse of the ocean. Quite the opposite, Mr. J (whose name has been changed to Husband) is more than eager to spend the night enjoying his honeymoon, oblivious to the rest of the world. He turns down her suggestions to go outside for a walk, and eventually she realizes that there is no escape. She goes into the bathroom to change into her nightgown. She emerges pale and terrified, and the stage goes black as she sobs and cries out for her mother or someone, anyone at all to come and save her.
Another skip in time, and the Young Woman is lying in a hospital bed after giving birth to a baby girl. Her Husband enters the room with flowers and she begins gagging as she apparently does whenever he comes to see her. Her nurse and her doctor quite obnoxiously attempt to diagnose her problem, and when the doctor suggests that they bring in the baby, the nurse informs him that the new mother has rejected her baby and done very poorly with her. As soon as the Young Woman is left alone in the room, she begins a tangled, disjointed, pleading speech about wanting to be left alone, left to rest.
Episode Five opens to a speakeasy some vague lapse in time after Episode Four. Two men sit drinking, waiting on their dates to join them. After a while, the Telephone Girl from Episode One enters with the Young Woman trailing behind her. For the first time in the play, the Young Woman is introduced as Helen, and the two men are identified as Mr. Roe and Mr. Smith. The girl and her date soon exit, leaving the Helen alone with the attractive and mysterious Mr. Roe. He quickly charms her with stories of freedom and living on his own. He even admits to killing two Mexicans with a stone-filled bottle when they tried to hold him captive. By the end of the scene, he has convinced her to leave with him and go to his apartment.
Episode Six begins with Helen (now called Woman) and Mr. Roe (now called Man) lying in bed after they have just been intimate. He is whispering sweet nothings into her ear, while she imagines that they will belong to each other forever. She is lost in his descriptions of a life full of freedoms and new places; trapped as she is, she does not have the freedom to see wide open spaces like the Rio Grande or the hills of San Francisco. They lay there singing and laughing together until she realizes the hour and must go. As she leaves, he lets her take a lily that is growing in a bowl filled with stones.
When the next episode begins, there is no sense of how much time has passed since the affair. However, the Young Woman is clearly upset and continues to make references to news articles about women leaving their husbands. When her Husband speaks to her, her responses are robotic up until he pinches her cheek and she flinches. There is a sense that she wishes to tell him what she is thinking, but she holds back. Suddenly, she grabs at her throat and tells him that she feels as though she is drowning. His solution is to condescendingly tell her to breathe. At the end of the scene, she is lost in a daze, hearing the voice of her lover combined with other anonymous voices. They repeat the words "stone" and "free" over and over until she cannot take it and screams just before the lights go out.
The Husband is now dead, and the Young Woman, Helen Jones, is on trial for his murder. She attempts to convince the Lawyer for Prosecution, the Jury, and the Press that her late husband was killed by two, big, dark men that came into their bedroom and killed him in his sleep while she lay next to him. However, she repeatedly stumbles over her story. The Prosecution finally traps her when he notes that Mr. Jones was bludgeoned by a bottle filled with small stones, and she had in her possession a bowl filled with small stones that used to have a lily growing inside of it. The Prosecution presents an affidavit signed by Richard Roe, confessing that he and Helen Jones had an affair for over a year and that he gave her the bowl filled with pebbles the first night they met. As the lawyer reads off the affidavit, the Young Woman cries out her confession, explaining that she only wanted to be free.
The final episode takes place on the day of the Young Woman's execution. A Priest prays for her as a Negro sings. The Young Woman begins to panic and asks, "Tomorrow! Father where shall I be tomorrow?" (9.64). She only asks for peace and rest, the kind of peace and rest she has not known in life. She wonders why she must die for the sin that finally made her free, if only for a moment. When her Mother enters, she screams at her in anger, telling her that she has been a stranger to her. Her attitude, however, quickly switches and she calls out for her Mother, begging her to take care of the daughter that she will never know. The Young Woman's last words are the same words she cried out on the night of her honeymoon, "Somebody! Somebod-" (9.163). The Priest asks for mercy, and the lights go dark.