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The Baroque Cycle can be seen as a sort of loose prequel to Cryptonomicon, though again, neither depends upon the other. There is a minor character who appears in both books, and I suspect the large stores of gold appearing in each book are also one and the same. There's also a strong thematic connection between the WWII portion of Crypto and much of TBC, as both revolve around the actions of eccentric scientists and mathematicians, at least some of whom are making early attempts at computers. It's been years since I read Crypto, and I suspect having read TBC will cast much of it in a different light.
Again though, the stories are quite independent.
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