What is the connection between Severian's story and Silk's?
The Book of the Long Sun starts in a place seemingly unconnected to The Book of the New Sun. Is Severian the god Pas? Was the Long Sun Whorl begun by Severian?
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The Long Sun Whorl was created at the command of Typhon, the ancient two headed monarch whom Severian defeats in Sword of the Lictor.
He is, in fact Pas, or rather Pas is a "copy" of Typhon uploaded to the Long Sun's systems (Mainframe) as King of the Gods with his wife & family as the pantheon. They all fall out & they erase him from the Mainframe. At one point this is explained in Lake of the Long Sun, without Typhon being named as such. I'm sorry that I can't offer a clear citation, but there is definitely a reference in one of the books of the long sun to "Two Headed Pas," which must be more than coincidence.
There is some discussion of this in Attending Daedalus: Gene Wolfe, Artifice and the Reader by Peter Wright, Liverpool University Press, 2003. You can find a pdf of the book here, it's well worth a read, even if you don't necessarily agree with all his conclusions.
The two stories appear to take place in the same universe. Pas is not Severian, he is some sort of uploaded personality derived from the tyrant Typhon (who Severian meets briefly in Sword of The Lictor). The Whorl is a colony ship launched during Typhon's reign, many years before Severian is born.