Quotes that explain his relationship from any chapter in the book
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For much of the book Eli is a devout Jew. He is steadfast in his belief in God despite the unspeakable trials that he must endure. As the novel progresses Eli sees more of his people suffer unspeakable horrors. He begins to question what kind of God can let this happen,
"Never shall I forget those moments which murdered my God and my soul and turned my dreams to dust. Never shall I forget these things, even if I am condemned to live as long as God Himself. Never."
I don't think Eli ever really forsakes his belief in God rather than reassess his faith and God's role in a world that holds much evil.