According to Cedric 'Inoxx' Fiorentino, technical limitations of the engine were the reason of why the Skaarj Generator exploding sequence had to be divided into two different levels (Skaarj Generator and Illumination).
"I think I frightened a lot of people with the Pupae in the Skaarj Mothership (you know those awful 4 legged spiders). I have to confess that I got scared several time in my own level.
One of the biggest advantage of the single player mode, is that you can have a progression. That's one of the main element when you design an adventure. It also allow you push the limit of the engine. For example in Unreal, you walk in this big Mothership, then you reach the Skaarj Generator and you destroy it. Then you go back to the Mothership which is unpowered. All the lights are gone, all the magnetic fields that locked the prisoners are off, all the lifts are broken.
This is not possible to do in a single Unreal level, especially the lighting part. You would have to use dynamic lights for the whole level and it would be terribly slow. So what I did is several copies of the level, one with lights, the other without light and you walk from one level to the other without noticing."