Typoes: "times a wasting" should be "time's a-wasting"; "what she hit" should be "what she had hit"; "what looked like crisis-torium" is missing a "the"; "as she watched the enormous eyeball move around on that gigantic, round eye" doesn't really make sense; "That would have been something to see those times" feels like it should have a comma after "see"; "grabbed a water tower off of the roof" doesn't need the "of"; "You know something,'" has an unnecessary single quote mark at the end; "why the Professor insisted on installing" should be "had insisted".
"I didn't ask you to believe in it - I just want you to deliver it.
You're missing a quotation mark at the end. Also, the start of one paragraph (the one starting "No one could ever say that John Zoidberg died without a fight!") is missing an indent.
For starters, I'm glad that you decided to revisit these ideas, because this is a pretty great concept for a story. Turns out it lives up to its promise, as well. I particularly enjoyed the Evil Universe, but pretty much all the storylines were good. The whole thing felt a lot like the show.
It's the comedy that really makes this fic shine. I don't think I've found any of your other stories as funny as this. The opening scene with Morbo is a hoot, and there are many hilarious jokes and scenes throughout. There are too many to point out, really. You have some great slapstick in the Lilliputian storyline, Amy gets some two-inch badass moves in her story, the Evil Universe is funny in its over-the-top evil, and Morbo is consistently good in all his appearances. I like the little "1984" reference, too.
Everyone seems to be in character; at least I didn't notice anyone being out of character. As for new characters, I like Evil Fry.
I frankly couldn't find many flaws in this story. It's a bit dialogue-heavy and lacking in description in places, especially on the first couple of pages, though you get a bit more descriptiveness later on, as the other universes are introduced. (And some of those descriptions are very atmospheric: I particularly like Fry's first glimpse of the alternative office.) Zoidberg's storyline felt a bit dull compared to some of the others, though the ending was sweet. (And that's not a flaw, it just shows that the others were better.) A couple of jokes felt a bit tame, but there were more than enough good ones to make up for it.
Finally, I really like your cover art for this. Excellent idea for a picture, and Leela's expression is great.
Definitely one of your funniest stories so far, with a very nice concept and several enjoyable adventures for the cast. Highly recommended. A