There are many, many different ways the world could end. Because we're more creative than the average person, we supervillains also happen to be a great deal more deranged. This means that we're quite good when it's time to come up with creative and exciting ways to make the world go kablooey. To list only a few, the world could end via:
Any number of problems relating to the Sun
Not enough pollution
Ancient artifacts (see above)
Gods (angry, happy, lazy, etc.)
...I hate that last one.
As you can see, there is no shortage of ways to dispose of a planet and all of its annoying inhabitants. It doesn't even have to be hard. During the creative process, writers and supervillains alike can plan on either starting or finishing the story with such an event. It could be like that movie 2012 where things blow up all throughout the movie, or like The Day After Tomorrow where everything happens toward the beginning and just kind of ramps up. It could also be like Ladder 49 where the firefighter dies at the end. Oh no, did I spoil that for you?
I'm so painfully wicked.
Technically I don't think that killing off a firefighter (portrayed by Joaquin Phoenix no less) counts as an evil plan. It doesn't take a mastermind to see that killing off one character is small beans compared to the main course of the evening, and that is cracking a planet in half, or in thirds, or other wonderfully evil fractions.
Sometimes it's not even the “event” that you're trying to write about. Some movies and books actually take place a long time after the world has ended. As you might imagine, it's referred to as post-apocalyptic, which is kind of a misnomer because the actual apocalypse from the Bible is kind of a one-off. Nobody walks away from that one.
I guess it's not really a (capital) Apocalypse you want; it's more like an unpocalypse. Or an apocalypse lite. Like the beer. I mean, what's the point of killing everyone if there's nobody around to notice? Sure, the reveling by the person who pulled it off would be wonderful for a while, but without civilians to look sadly toward the burned-out husks of buildings, what's the point?
That's not to say I wouldn't mind a good reveling.
The real trick is leaving enough main characters alive long enough to give the audience a (false) hope that he'll give this miserable story a redeeming ending. You would think that after the freaking apocalypse the guy's story would end, but it never seems to. If you're too cowardly to actually blow up your universe, I suppose you could just threaten to do it a bunch of times throughout the main character's journey. He'll probably try to stop it, and he'll probably win, but at least you kept the tension on him.
Still, when it's time to make like The Matrix and make the world an awful place to live, you might as well do it right. That's actually a good example of what a story can look like when the bad guys kind of win. As long as you ignore the second and third movies and all of that strange Matrix Online story stuff they threw (up) into the lore.
Someone should really try writing more stories from the perspective of the quote unquote bad guys. That's right, even though I'm writing, I still used air quotes as if I were actually talking. Into your brain.