The "harvested for ancient energy" bit, yeah, ~200 hours of looking at the architecture 'n stuff.

The basic idea... Not really?

• Something happened to Ganon that made him begin "reincarnating" as Calamity Ganon, all normal forms of him are spoken of as phenomenally ancient legends
• We see an extremely ancient corpse that is clearly Ganondorf sealed away with a much more pure version of Malice leaking from it

There's more evidence about the specifics of why he might be down there than that, but the basic idea of "oh crap the real ganondorf was down there?" is something that anyone paying attention should've picked up on pretty much immediately