The underground, high-tech laboratory complex where the cause of the apocalypse originated.
You can fit a lot of details into that theme that reinforce your group's connection to the history of the setting. Parts of the complex will still be working; parts will be in ruin; evidence of the apocalypse's genesis will be available in some locations, allowing your players (if not the characters) to get glimpses — and a dawning realisation/horror — of what may have happened. You could even have apocalypse-related things here that haven't shown up (yet) on the surface – this is where it all went down, so there may be unique and especially weird lingering effects or creatures.
And because it's a megadungeon, the PC party may spend months or years of game sessions delving before you have to worry about "giving away" every secret of the apocalypse, and the prospect of learning more is a great secondary (or even primary!) motivator for the players to engage with the location with extended exploration.
Possible things/regions of such a megadungeon:
- Remnants of experiments that were running when the site became Ground Zero
- Still-working (or mostly working) automation, including possibly robots and (insane?) AI
- Where the scientists and workers lived on-site
- Supporting industrial bases that the complex had to be more self-sufficient
- Administrative areas
- Areas of the complex that were abandoned even when it was still being used – you could get layers of history in this way
- Failed experiments, or sealed-off areas quarantined, some now exposed by the post-apocalypse, or otherwise accessible by people who don't know the proper containment procedures when entering (such as the PCs)
For inspirations, Valve Software's Half-Life (the first one) and Portal 2 games feature strongly-themed environments based on technological research complexes that were implicated in, or directly impacted by, an apocalyptic event.