I just played a game in which Fanatic, with 1HP, evoked End of Days. One of the cards she destroyed was an Explosives Wagon, which damages all targets when destroyed. Does the damage happen right then in the middle of resolving End of Days? And if so, does End of Days's effect end the moment Fanatic falls, removing all her cards from the board?
Yes and yes.
Can Fanatic die in the middle of an End of Days?
Yep, anything that triggers on destruction interrupts the End of Days and you deal with that effect 'now', which could kill her (or end the game in Akash's case).
Would it wipe out EoD?
I don't see why not, all cards belonging to a character are removed, no matter where they are (as previously clarified by the under-La-Capitan incap situation).
So what you'd have to do for best effect would be to have End of Days destroy all the villain stuff first, plus anything else you didn't want sticking around, then go on to the Explosives Wagon, which kills Fanatic and thus causes all of her cards to be removed from play, including End of Days. It's much the same as when you use it (End of Days) in a game with Unity when she has a Bee Bot out - make the Bee Bot the first hero target to be destroyed (after all the villain stuff and any unwanted environment cards have been dealt with) and then have the Bee Bot's destruction take out End of Days so that everyone gets to keep all the rest of their stuff :D.
You could also use illusory demon for that purpose
Or the Matriarch.