As a conceit can be defined as an elaborate metaphor, and Spenser claimed "dark conceit" to be a synonym of "continued allegory," he uses the term to define the nature of his book as an allegory.
An allegory uses characters as symbols, often to express a moral or political truth. In his case, Spenser uses the story to express ideas about Elizabethan politics, while certain characters represent different religious virtues.
In his introduction, written as a letter to Sir Walter Raleigh, he says:
Sir, knowing how doubtfully all allegories may be construed, and this book of mine, which I have entitled The Fairy Queen, being a continued...
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