Jocelin, the Dean of the cathedral, directs the construction of a towering spire funded by his aunt, Lady Alison, a mistress of the former King. The project is carried on against the advice of many, and in particular the warnings of the master builder, Roger Mason. The cathedral has insufficient foundations to support a spire of the magnificence demanded by Jocelin, but he believes he has been chosen by God and give a vision to erect a great spire to exalt the town and to bring its people closer to God. As the novel progresses, Golding explores Jocelin's growing obsession with the completion of the spire, during which he is increasingly afflicted by pain in his spine as a result of tuberculosis. Jocelin interprets the burning heat in his back as an angel, alternately comforting or punishing him depending on the warmth or pain he feels. Jocelin's obsession blinds him to reality, as he neglects his duties as a dean, fails to pray and ignores the people who need him the most. The pit dug to explore the foundations at the Cathedral crossing becomes a place where chthonic forces surge, as the four tower pillars begin to 'sing'.
Jocelin also struggles with his unacknowledged lust for Goody Pangall, the wife of the crippled and impotent cathedral servant, Pangall. Jocelin seems at first to see Goody as his daughter in God. However, as the novel progresses, and Goody's husband is tormented and ridiculed as their 'fool' by the bullying workmen, Jocelin becomes tormented by sexual desire, usually triggered by the sight of Goody's red hair.
Comparisons between Goody and Rachel, Roger Mason's wife, are made throughout the novel. Jocelin believes Goody sets an example to Rachel, whom he dislikes for her garrulousness and for revealing her marriage to Roger remains unconsummated because of their inappropriate humour at each sexual encounter prevents it. However, Jocelin overestimates Goody's purity, and is horrified when he discovers Goody is embarking upon an affair with Roger Mason. Tortured by envy and guilt, Jocelin finds himself unable to pray. He is repulsed by his sexual thoughts, referred to as " the devil " during his dreams.
The Cathedral building, its ordered life and the lives of the people around Jocelin are disrupted because of the intractable problems arising from the construction of the spire, but Jocelin continues to drive his dream to its conclusion. His visions and hallucinations, hence his denial of the reality of the situation, mark his descent into irrationality. As the true costs, financial and spiritual, of the endeavour become apparent, the story moves to its tragic conclusion.
Pangall disappears, although his fate is never made explicit it is clear from the clue of the mistletoe that he was a pagan sacrifice buried at the Crossing by the builders to secure their luck against the stupidity of continuing the work. Goody Pangall dies in childbirth, bearing Roger Mason's child. Roger becomes a drunkard and at the end Jocelin dies of his illness, though only after first hearing from his aunt that his appointment was due only to her sexual influence, not to his merits. Before he dies, the phallic imagery of the Spire is displaced by the mysterious symbol of the tree. The spire is incomplete at the end of the story, and there is a growing sense of impending disaster due to the instability of the over-ambitious structure.