Janeway tells Chakotay that she met aliens with really advanced technology who have outlawed warp drive. She tells him she has managed to make an agreement where they can keep their ship but must surrender their warp core and settle on a planet.
Janeway asks B'Elanna to make some modifications to the Delta Flyer. B'Elanna asks Chakotay to speak with her. Chakotay speaks to Janeway on the bridge but she leaves. She is asking strangely and talking to herself.
Chakotay asks The Doctor to throughly examine Janeway. Voyager gets a call from the aliens telling them eject the core. The Doctor tells Chakotay that Janeway is fine.
Chakotay discovers it is not the real Janeway but she stuns Chakotay with a hypo spray and puts him in the morgue. Janeway turns out to be The Doctor. He makes a comm call. The real Janeway is being held hostage and the aliens are blackmailing The Doctor.
Tuvok asks to see Chakotay and The Doctor turns into him. Later The Doctor turns in B'Elanna and heads to engineering and keeps themselves to a few jellpacks. Tom interrupts with food but The Doctor gets rid of him eventually.
Seven and Harry tell Chakotay that the alien message telling them to eject the warp core came from Holodeck 2. Harry discovers it was The Doctor but he is taken out and is soon in the morgue along with Chakotay.
The Doctor manages to take control of the ship and eject the warp core, escaping with it in the Delta Flyer. He arrives at the aliens ship but they take the warp drive and beam the Doctor aboard, taking him hostage too.
Tom finds Harry and Chakotay in the morgue. B'Elanna gets main power back online and The Doctor's music starts playing all over the ship. It contains a message telling them where The Doctor has gone. Tom and Tuvok take a shuttle.
The Doctors programme is having a problem when the aliens upload new information and starts to decompile. Meanwhile Tom and Tuvok arrive in the shuttle. Tom beams aboard the Delta Flyer and together they attack. Janeway, The Doctor and the second alien who has become friends with them take control of the ship.
Once back on Voyager the crew battle to stop The Doctor decompiling. He thinks he is going to be lost and makes several confessions however B'Elanna manages to save him. His programme is saved although his pride is not so stable.