He developed a fondness for Kes and asked her to leave Voyager and travel with him. He took Kes on a romantic walk and kissed her. The next day Kes asked Captain Janeway for a leave of absence, so as to travel with Zahir in his ship to explore the Sylleran Rift. Later, Zahir was walking the same path when he was attacked by a cloaked figure who knocked him off a cliff, seriously injuring him.
It was later revealed that he was attacked by The Doctor who, in trying to enhance his program, had created a second, evil version of himself that had taken over The Doctor's program at some point. He had become insanely jealous of Kes' relationship with Zahir. With medical help from Voyager facilities, Zahir quickly recovered, and Kes decided to stay with Voyager. (VOY: "Darkling")