More ideas from Tricky's brain...
Ok, this idea isn't as fleshed out as some of my other ideas have been, mostly because I'm super tired from work. I was thinking about a quantum fissure; which according to at least one TNG episode can lead to alternate realities. I was wondering what the FED would do if they found a fissure that was acting more like the Bajoran Wormhole: permanent and acting like a doorway. One random part of the idea was that it started out an anomaly on a survey mission, and a ship was tasked to study it. As they studied it, it seemed to get stronger (was it their ship opening up the fissure, or was it something else?). Pretty soon it's letting small bits of other universes into the Trek one.
Fast forward a bit, and it now opens much bigger. A station has been placed nearby, to study it better, meet explorers from the other side, help out entities that have been lost in the Fissure, and above all, protect their home universe.
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"Yes, it's the Apocalypse alright. I always thought I'd have a hand in it"
Professor Farnsworth