The Guardians narrates the journey of Rob Randall as he gradually becomes aware of the truths about his world and his role within it. It is revealed that Rob's father had been part of a plot to overthrow the Guardians. However, for his own safety, Rob was raised to be as similar as possible to any other boy in the Conurb. Following his father's death and his own enrollment at a strict state boarding school, Rob finds life in the Conurb unbearable. He eventually escapes to the County, where he befriends Mike Gifford, another boy who has also managed to resist some of his societal conditioning.

With Mike's mother agreeing to help, Rob is welcomed by the Gifford family and is introduced as a distant relative from Nepal. Starved for privacy, genuine education, and emotional connection, Rob grows to love his new life and family. Meanwhile, Mike begins to scrutinize County life more critically and becomes involved with a group of student activists planning an unsuccessful uprising. Mike seeks Rob's help to escape to the Conurb—a plan Rob is willing to keep secret but not join himself.

There were no crowds, no feeling of being part of a noisy group that could provide mutual reassurance and safety.
It is only in the final pages of the novel that Rob starts to confront the reality of his situation. Authorities declare that his disguise as a distant Gifford cousin was detected immediately; he was allowed to stay in the County as part of a government experiment, and he could now expect to remain there for life as a Guardian. Experiencing security for the first time, Rob agrees to become a Guardian. However, he is disturbed to learn that The Guardians plan to conduct brain surgery on Mike once they capture him, just as they did on Mike's father when he was Mike's age.

Rob understands that The Guardians have offered him "the chance to be not a puppet, but a puppet master." His challenging decision to reject The Guardians and return to the Conurb as an activist has an unexpected and immediate impact. Rob recalls the many times in his childhood when his father would abruptly leave, leaving him hurt and confused. Now, finally, Rob feels "a strange sense that, after all, things had turned out right. He was going with his father, long years behind but following."