[archy]

It would be quite interesting if they were using a suicide submarine as a delivery system for a crude nuclear device in San Francisco Bay.

The nuclear weapon aspect would certainly explain the secrecy lid clamped on the sub's presence. And the Germans had a design for an A-bomb that didn't require a great deal of refined plutonium, just the more common U-235/U-238.

Hmmm, wasn't there a German U-boat shipment of German uranium *yellowcake* intercepted en route to Japan....?

[archy]

Hmmm, wasn't there a German U-boat shipment of German uranium *yellowcake* intercepted en route to Japan....?

Yep. Found the info. it was U-234

Additional U-234 info *here*. The Japanese officers aboard committed suicide rather than undergo interrogation by the US Navy.