During Season 2, Voyager suffered numerous conflicts with the Kazon-Nistrim following the betrayal of Seska. At one point, Jonas spoke out against Captain Janeway's policies on exchanging technology with any of the denizens of the Delta Quadrant, insisting that Voyager try and seek an alliance with the Kazon. Janeway flatly disregarded the idea, seeing all of the Kazon factions as dishonourable and treacherous, as they had proven in all of their past encounters.
Having lost faith in Janeway's leadership, Jonas secretly made contact with the Kazon-Nistrim and attempted to negotiate with them. He became an informant for the Nistrim and would regularly send covert transmissions to Seska informing her of Voyager's position.
In the episode "Investigations", Seska ordered Jonas to sabotage Voyager's magnetic constrictors so that they would be forced to head to the Hemikek system and land on a planet there in order to seek materials to complete repairs. Kazon-Nistrim forces would then storm the ship on the ground. Around this time, Paris asked to be put off the ship and signed up with a Talaxian convoy as a pilot. Neelix became suspicious, not believing the reasons for Paris' departure. Janeway and Tuvok quickly acted to stop him from exposing their deception, and asked him to announce that they had found Paris to be the traitor. Jonas fell for the ruse and contacted Seska about these events. Kazon-Nistrim forces attacked the convoy and kidnapped Paris. Recognizing Paris' value, Seska tried to convince him to join them. Instead, Paris broke into their computers, learned the identity of the traitor, and then escaped. He was able to transmit the information to Voyager just as Jonas was preparing to sabotage the ship. Neelix continued his own investigation and also discovered Jonas' treachery. A struggle ensued when Neelix was trapped in main engineering with Jonas and attempted to prevent the sabotage, but Jonas was killed as he fell into a plasma fire near Voyager's warp core.