In 2377, he became romantically involved with Kathryn Janeway, who had been kidnapped and brainwashed to think she was a laborer on Quarra. He met her at the power plant and asked her out for a date, which Janeway refused. Later, he encountered her again at a local bar and spent the evening with her. He walked her home from the bar and the two had dinner together several times, including one prepared by Janeway, when the two finally spent the night together at Jaffen's home. He later asked her to move in with him, which she accepted.
Later, when Chakotay tried to tell Janeway that she was in fact captain of the USS Voyager and had been brainwashed, she told Jaffen the story. He became jealous believing that Chakotay wanted Janeway for himself, so he informed the authorities about Chakotay. After he and Janeway came to believe Chakotay's story he helped her break into the power plant so she could contact Voyager using a subspace transponder in the plant. He protected her from the guards while she contacted the ship.
After Janeway and the rest of the crew had their true identity restored, she decided to return to her former life. She stated that she would have offered Jaffen a job in engineering, but it wouldn't be appropriate. He decided to give her an engineering trinket to remember him and the two parted ways after an embrace. (VOY: "Workforce", "Workforce, Part II")