Re: What happened with Kes and Neelix?
After the events of "Tuvix", where she pleaded with Janeway and finally got Neelix back, she realized what a disgusting horrible creature he was and asked for her lung back. He refused, saying he had salvage rights to it. Then she knew it was all over.
The actual breakup was never shown on screen. They just dropped it altogether.
Dr. Howard, Dr. Fine, Dr. Howard: For duty and humanity! --Men in Black (1934)