The bomb that ripped open Long Stair was "special". According to a recovered set of blueprints, its designers used gold instead of lead for the shields. Additionally, the blueprints bore pencil marks, erased and done over several times; comparison with features encountered within the Dungeon reveals noticeable similarities.
The Nevada test facility came under command of a Colonel Nolan Shepherd about three years before the Opening. Prior to this there's no service record for him; after the blast, he was "replaced", and drops off the face of the planet again.
Recently acquired information, highly classified and restricted, reveals that the plans were the discarded work of Nazi science spun out of PAPERCLIP and re-engineered.