The Hirogen have taken the holographic technology Janeway gave them once upon a time and improved it so much that the holograms are now a) sentient and b) killing them. The EMH’s loyalties are tested as Voyager is caught in a war between self-aware holograms and pissed-off Hirogen. The Star Trek: Voyager Rewatch is a thing of “Flesh and Blood.”
With all that, though, this two-hour episode doesn’t quite cohere. Part of the problem is that Iden is a nowhere antagonist. Jeff Yagher has no discernible personality (Cindy Katz and Spencer Garrett do a much better job), and his transition from bland affable leader to megalomaniacal murderer is utterly unconvincing. It’s a narrative cheat to make the EMH’s decision easier, but it makes the arguments far less convincing. The holograms generally are not the nicest people around—they kidnap both the EMH and Torres, they pretty much torture the EMH to make a point—but it was up to Yagher to show how they were evolving past that, and he never really did that. He was unconvincing as an antihero, as a resistance leader, or as a lunatic.