The Three-Body Problem begins in the middle of China's Cultural Revolution, a time in which academics and free thinkers were considered enemies of progress. Such intellectuals were often subject to public shaming and humiliation, and many were exiled or driven to suicide.

This period in Chinese history was characterised by bloodshed, thought control, and chaos. Those who dared to speak out against ideological oppression, let alone express ideas that could be arbitrarily considered 'reactionary', were summarily dealt with. The Cultural Revolution gave rise to many atrocities—some committed in the name of self-preservation, and others out of sheer cruelty.

One such atrocity sees Ye Wenjie, a minor academic, seeking shelter and anonymity in the remote Greater Khingan Mountains. There, she is drafted into the mass deforestation effort, her emotions numbed by trauma. She soon finds that nowhere is safe from the revolution. Falsely accused of a crime she didn't commit, she refuses to confess, and is left to die in a cell.

Rescued by an old acquaintance of her father's, she is taken to nearby Radar Peak, a high security military base. The facility, overshadowed by a large parabolic antenna, is said to specialise in defence research. Ye finds she has been scouted by the facility for an old research paper of hers, and is offered a position there as an alternative to her sentence. She is warned that once she steps inside, she may never be allowed to leave.

Bereft of hope and purpose, she enters the facility.

This small action sets in motion a series of events that will drastically alter the course of human history.