These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Colony Wars
Big Lipped Alligator Moment: Upon fighting the Widowmaker for the final time, the player is suddenly transported to a surreal place with wild shifting colors instead of stars. The Widowmaker splits into several smaller Widowmakers when he's destroyed, and those split into even smaller ones. This is neither explained nor ever referenced again.
This option doesn't exist in the canon path; with only Sol left to defend, the Navy has no logistical problems getting forces to the combat zone (this is mentioned as a contributing problem to their efforts in the Bankrupt ending, they can't pull enough forces from anywhere to keep fighting the League without those systems instantly joining the League) nothing to lose and nothing to sell the League besides surrender, which they aren't willing to do because they know Sol isn't going to fall. They were fighting so fiercely to get the League back out of Sol that the League couldn't take the system and would've had to retreat. Presumably, someone high up (likely the Father) decided that cutting Sol off was the lesser of two evils compared to prolonging the war further, because they aren't going to particularly care about the Empire's well-being after centuries of abuse and being looked down upon as slave labor for the benefit of Earth. Considering how much hate the Empire inspired and judging by the lack of division in the League over it come Vengeance, most of the League was probably just fine with it, and while it's not very nice, it's at least understandable why they would be.