There are three major themes in Ken Kesey's One Flew Over the Cuckoo's Nest:
Individual vs. Society
Much of the plot revolves around McMurphy's struggles against Nurse Ratched, who is dictatorial in her occupation. From the time that he arrives, McMurphy challenges the "democracy" of her group therapy in which she sadistically renders punishments later to those who speak out. For Kesey, the society of the institution became a microcosm of contemporary society in which conformity, too, was a means of upholding law and order.
Sanity and Insanity
In portraying the sane McMurphy's conflicts in the Acute/Chronic Ward, Kesey questions what is truly insane? When McMurphy asks some of the male patients why they have self-committed, one of them, Billy Bibbit, replies that he does not have the "guts" to get along in outside society. However, Nurse Ratched exacerbates Billy's condition by demeaning him and undermining his confidence, rather than trying to build it. These actions suggest that an authoritarian society wishes people to weakly conform and dehumanize.
McMurphy's war against Nurse Ratched is lost as she has him lobotomized. However, his rebellion against conformity inspires the other men. The Chief narrates,
She tried to get her ward back into shape, but it was difficult with McMurphy's presence still tromping up and down the halls and laughing out loud in the meetings and singing in the latrines. She couldn't rule with her old power any more, not by writing things on pieces of paper. She was losing her patients one after the other. After hrding signed out and was picked up by this wife, and George transferred to a different ward, just three of us were left out of the group tht had been on the fishing crew, myself and Martini and Scanlon.
Recurring images of shock patients and patients under seizure in positions of one who has been crucified reinforce this theme.