They were involved in the scenario where Captain Janeway and Lieutenant Paris were taking a shuttle for a 24-hour visit with the Rukani. Although a seemingly friendly species, Chakotay suggested that perhaps she should take Tuvok along in case they turn out to not be as friendly as they appeared. This was, however, Chakotay's attempt to get Tuvok off the ship.
After Seska's variation of the program took over the holodeck, Janeway reprogrammed a Rukani vessel to attack Voyager. Seska, who was not prepared for this change in the scenario, was surprised when Paris explained to her that he and Janeway had contacted the Rukani for assistance once they discovered word of the mutiny. (VOY: "Worst Case Scenario")