Location-based superhero adventures

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I saw the ad for Pamphlet Dungeon Jam and of course it had me thinking of superhero adventures.

Superhero stuff tends to follow a villain rather than a place, so location or dungeon based adventures are rare. In general, I can think of these cases that show up more than once:

• Lairs — This is the hero lair, which has defenses which have turned against them, or the villain lair, which has defenses to keep the villains out. You certainly can do it as a separate adventure, but the villain lair tends to be the climax of the adventure, after other stuff.
• The crime scene — The entire adventure can be wrapped up with one attempt. For instance, you could do an entire adventure based in a museum, for instance, where the heroes know the bad guys are coming, but they don't know for what. Or there are two attacks at the museum the same time: maybe one is a diversion for the other, or maybe it's two groups trying for the same thing, and they fight while the heroes try to figure out how to stop them and protect the innocents, or even it's just a coincidence but they decide to team up and take on the heroes.
• The special place — Something like Fainting Goat Games' "Helicarrier Heist" would fit here, or maybe one of the adventure seeds with the Green Ronin Mutants & Masterminds Freedom City maps. (One could consider the lair situation to be a part of this, but I think it deserves its own category.) I'd put the superjail-gone-bad here, too.

Any of these would do for comic stories, especially before things became so decompressed, but for RPG adventures the first and third are most common.

The concept that appeals to me right now is the supervillain lair, but as a dungeon in itself. That is, you're not going to run up against the original owner. No, he's been caught and in the process seriously weakened the most powerful heroes in your campaign world (who aren't the PCs). And now the PCs are tasked with deactivating the base...because he left contingency plans that would launch the world-wide disaster.