Prior to filming this episode, there was some doubt as to whether NBC would agree to more episodes. An alternate ending was written (but not filmed) in which Bogg would have saved the lives of Jeffrey's parents, giving the series a somewhat satisfying ending. See more
We must now weigh the evidence presented here. And our decision will affect not only the career of Voyager Phineas Bogg and the future of young Jeffrey Jones, but of the fate of all Voyagers. Of course, ultimately, we're charged with upholding the Voyager Code and the safety of the past, present and future, which that code and all Voyagers are sworn to defend.