I've been watching the first few episodes of Voyager's season four and I just finished Scientific Method. I had a crazy thought when B'Elanna and Tom talked about how their love could have started due to the alien experiments. She mentioned they had no idea how long the aliens were aboard.
What if Kes' situtation was brought on by those aliens. Scientific Method takes place about two months after Seven was freed from the collective.
Surely Kes would have been of interest early on. They never concluded what started Kes' transformation.
The Year of Hell took place right after this. That may mean those aliens were in a less advanced state in the timeline of Before and After. Those aliens would be fairly close to Kremin Space. Annorax must have done something to the timeline that helped those aliens become more advanced to the point they could do such experiments on unsuspecting ships.