After Janeway and Paris leave on an away mission, Chakotay leads a Maquis takeover of Voyager. With Torres' help, he seizes control of the ship and vows that Federation principles will no longer stand in the way of getting the crew home. Just then, Paris walks in and asks Torres what's going on. Annoyed, Torres freezes the holodeck program she's been running — the whole mutiny scenario was part of a holo-novel she's just discovered.
The identity of the holo-novel's author is unknown, but Paris is fascinated by the subject matter. He resets the program and replays the mutiny with slightly different plot twists. Just as the holo-novel appears headed for an explosive climax, the program abruptly stops and Paris learns that the writer never completed the story.
The program is soon the talk of the ship, and Tuvok finally admits he's the author. He wrote it as a tactical training exercise when the Maquis and Federation crews first merged. Since the union went smoothly, Tuvok didn't bother finishing the program. After Paris volunteers to complete the tale, Tuvok decides to collaborate with him. But when they re-open the narrative parameters file to write the final chapter, a holographic version of Seska appears; the real Seska discovered Tuvok's program before she left the ship and decided to finish it the way she thought it should play out. She tells Tuvok that she's sealed the holodeck and deactivated the safety protocols; if she shoots them, they'll die.
Although she gives them a brief head start, Tuvok and Paris find that Seska's scenario is deadly. What's more, Seska has laid booby-trapped subroutines, which means that one wrong move could destroy the ship. Outside the holodeck, the crew discovers Seska's schemes and tries to find a way to help Paris and Tuvok.
As Seska prepares to execute Tuvok and Paris, the real Janeway works furiously to rewrite the program. Her efforts throw Seska off just enough that Tuvok is able to rig a phaser malfunction, which kills Seska, ending the program. Safely back from their ordeal, Tuvok and Paris congratulate Janeway on her literary skills and the crew begins planning a new holo-adventure.