"Silence" is a historical novel set in the 17th century, which follows a Portuguese Jesuit missionary who travels to Japan to comfort local Christians and find his mentor, who is rumored to have renounced his faith. The protagonist experiences the brutal persecution of Christians by the Japanese government, and grapples with the silence of God in the face of suffering. The narrative explores themes of faith, doubt, cultural clash, and the human capacity for both cruelty and endurance.

The book follows Lucas Corso, a book detective who is hired to authenticate a rare manuscript by Alexandre Dumas. As he delves into the investigation, he finds himself entangled in a mystery involving two other books: a rare edition of "The Three Musketeers" and a satanic text, "The Book of Nine Doors of the Kingdom of Shadows". The narrative becomes a complex puzzle as Corso uncovers connections between the books, while also dealing with a seductive woman who seems to have stepped out of a Dumas novel, a mysterious killer, and a group of bibliophiles obsessed with Dumas. The lines between fiction and reality blur as he gets closer to the truth.