Since we never got to see it happen on screen, we can pretend it happened this way (adapted from 1989's The War of the Roses)
NEELIX: I think you owe me a solid reason. I worked my ass off for you to have a nice life and you owe me a reason that makes sense. I want to hear it.
KES: Because. When I watch you eat. When I see you asleep. When I look at you lately, I just want to smash your face in.
And after running this through the sweetness and light translator it would come out: "we have grown apart, you deserve someone who can be with you for who you are".