VOY Season 2 Summary . Season two of embraces a slightly darker and more serialized tone than that of season one . Recurrent themes of tension and mistrust between the Starfleet and Maquis crew s , although largely resolved in the season one episode , once again resurface in and . Inter - crew relations are brought to a head while under intense , continuous attack by the Kazon in , and when Janeway is cajoled into initiating a Maquis - led idea of a deal between the and the warring Kazon factions , narrowly averted disaster is enough to quell the two crews into a marriage of Starfleet ideals and ethics . Indeed , increased , and more dramatic conflict between " Voyager " and the Kazon is the main feature of the second season , aided and abetted as the Kazon are by the vengefully villainous and by now , more Cardassian looking Seska . Her vendetta against Janeway brings " Voyager " to the brink of destruction more than once during the season in , , and , and culminates in the season finale when " Voyager " s crew is marooned by Seska and Culluh of the Kazon - Nistrim on a world inhabited by creatures and prehistoric humanoids . Alongside the Seska / Kazon story arc of the second season sits another spy in " Voyager " s ranks . Michael Jonas , a disillusioned former Maquis crewmember assigned to engineering is revealed to have been secretly communicating with Seska as she attempts to seize control of " Voyager " . Events leading up to the exposure of Jonas traverse the entire middle of the season , as does Tom Paris ' apparent malcontent and ultimate decision to leave " Voyager " ( revealed in as an attempt by Tuvok and Janeway to ascertain who the spy is ) . With Seska and the conflict with the Kazon as central themes , the rest of the season continues to develop the main characters , and more particularly their relationship to each other . Of singular note is the birth ( in ) of Ensign Samantha Wildman ' s baby , Naomi , but firm bonds and friendships develop between individual crew members as the series continues to evolve and find its feet . A connection between Paris and B ' Elanna Torres is hinted at as she confides past mistakes to him and communicates concern at his increasingly errant behavior in . Paris also finally makes peace with Neelix when forced to work together to ensure their survival in . Kes and The Doctor ' s relationship solidifies in and , and Kes ' s trust in Tuvok is pivotal when dealing with her burgeoning and uncontrollable mental abilities in . Tuvok and Neelix continue to make the perfect " odd couple " but their pairing takes on special significance when a transporter accident fuses them into a single being in . Finally and conclusively , Janeway and Chakotay find a common understanding , and any allusions to a romantic interest between the two is finally laid to rest in . " " I didn ' t feel as if I could have a love - affair with the second - in - command because , I had to get these people home . . I got them lost , and I really couldn ' t be doing things in the Ready Room " " : – Kate Mulgrew ( speaking at Sacramento , USA Convention 2003 ( uploaded on YouTube ) ) A few of these relationships , though in their infancy in season two would go on to become increasingly important as the series moved on . Season two encompassed a dark time for the franchise , with dwindling audience numbers , and still no obvious signs of a singular direction producers wished the series to go in . Problems of direction can be seen with the one and only appearance of the female Caretaker , Suspiria , which was included as a possible " get - out " clause should the series ultimately fail . Appearances by John de Lancie as Q and Jonathan Frakes as William T . Riker in were obvious attempts to re - invigorate the series , but episodes such as where Paris breaks the warp 10 barrier and evolves into a " salamander " did little to silence " Voyager " s critics . It is perhaps indicative of the conundrum facing producers at the time , that the heavy reliance during the second season on stories involving the Kazon ( never a popular species with fans ) was quietly relinquished as " Voyager " moved beyond Kazon territory at the start of season three . The species would be revisited retrospectively in season seven ' s , but apart from brief appearances in season four ' s , season five ' s and a couple of conversational " nods " in season four ' s and season five ' s , the Kazon were not heard of again . Credits . Cast . Starring Also Starring Crew . 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