OK. Oooookayyyy. That waterfall's a bit much, isn't it? Let's revise a bit. Clearly this is not a building, it's a The Last Of Us level. Maybe one of the Far Cry games, or even something in the Uncharted universe. Either way, sorry in advance, friend -- no matter what the protagonist calls himself, he's going to be a damn one-man army, and everyone's going to sound like either Nolan North or Troy Baker. Hope you have approximately 2,000 mooks who don't mind hiding in cramped corridors for days on end at your disposal. Not that they'll help, but an extra five minutes of life is an extra five minutes of life.
Still, on a positive note: No matter how well you plan and execute your nefarious deeds, we both know that somehow, some way, you're going to get thrown off that damn waterfall. So just take up base jumping and wear a parachute 24/7, and you should survive to see the sequel with just a badass facial scar or 16.
Let's say you're one of those overly specific villains who can only function in a very particular environment or situation. No, not quite Calendar Man level -- if you're that far gone, the only headquarters you're going to need are the ER and your familiar cell at Arkham Asylum. I'm talking Mega Man villains, or maybe even Pokemon: vast power, only within the confines of very specific elements. Like if you were somehow both grass and water type.
I'm not necessarily saying that I have anything to accommodate such ridiculously limiting bullshittery. However, if that's the way you really want to go, I might just casually nod my head toward SS Ayrfield.
It's like Noah's Ark, but for trees.
A century or so ago, this massive-ass coal freighter was abandoned in the Homebush Bay, which was then contaminated with toxic waste because fuck you, just because it's a ship doesn't mean that it can't get a Joker-style origin story. Eventually, the bay got less toxic, and nature started eyeing the ship. Stuff took root and started growing, and before you knew it, two things long neglected by man had formed an unholy union that you just know can start whipping spiked vines at your enemies as soon as you reach the captain's cabin and find the flute that commands this naval jungle.
And here's the thing: By settling in and learning to control SS Ayrfield, you don't gain just one ship: You'll have an entire navy. The Ayrfield has three compatriots rusting away at the bay. The Heroic, the Mortlake Bank, and the Karangi are just waiting for the right megalomaniac to control them. And if for some reason it turns out that the ships are just dormant wrecks instead of toxin-infused haunted ships waiting to take their revenge, well, you still have the high ground. You can just do that annoying Metal Gear enemy thing where you jump around from place to place (or, in this case, deck to deck) as the elderly, monovisioned, inexplicably snake-themed mercenary chasing you rapidly finds out that his limited depth perception isn't worth jack shit in a combined jungle/marine environment.
And if you want to expand beyond Homebush Bay, there's roughly a hundred wrecks laying around nearby.