ideas hollow earth gave me

I never thought I'd jump on the Agharta-Bandwagon, well here goes...

Admiral Byrd landed, saw the Haunebus in operation, was captured, and given hallucinogenic drugs.
Nazis took fuel from his plane (missing fuel adds to more flight time) because they needed it, but left enough to fly back.

The Player can talk to him, but he just rambles and spouts new-age gibberish. (frequencies, dimensions, higher states, hears&smells colors, battles of the light beings with the dark sentient fungi, etc. The Nazis may have had a good long talking to him to instill as much garbage as they could.)
The Player can free him during the last mission, but has to constantly watch over him, as he wants to go talk to the 'light children' and fly with them to 'Agharta, the inner dimension of the vibrant earth'. (If the player doesn't, Byrd somehow escapes alone, and meets up with the Player at the end. If asked how he got away, he says some incomprehensible nonsense involving higher states, fluxoms, , and that he was 'guided by the wise hands of the light-beings' (The Nazis probably set him free to ensure no straight story gets out there)

This explains why he is such a nut-job once he reports to his superiors, and how the player's story gets discredited. (two different stories, one harder to believe than the other)

Might be wise to change the name of the good Admiral slightly (?) Baird comes to mind.

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'Agharta' is the Nazi codename for the underwater passage under the ice of Antarctica to the base.
As seen in this youtube series:
They have some nice (scans?) of documents, and relatively accurate translations. Could be fakes though. (wish they had links to better copies)

They created all the inner-earth maps to throw off any intelligence gathering.
The Spy could have originally been sent to try to find out more about Agharta, inner earth, etc. Just in case...

You could maybe throw in an ancient bunker or two. Titan Dome, Antarctica, seems to be a decent place to put a huge hollow chamber. Maybe the ancients built these in order to survive the recurring cataclysm that is claimed to have struck the earth 10000 years ago (the video-series mentions it, but they're basically referring to the Nibiru-garbage). Whether or not the garbage turns out to be real, placing redoubts under the ice makes sense, as the massively thick sheets of frozen water will effectively stop deadly neutron radiation. (a fact that usually places nuclear bunkers under bodies of water)