“Projections” is episode three of season two of Star Trek: Voyager.
The Doctor activates in a darkened sickbay to find no-one there. He asks the computer who activated the EMH and is told it was auto initiation following a ship wide red alert. He tries contacting the captain and gets nothing. The computer states that Captain Janeway is not aboard the ship. In fact, no crew is onboard.
The location of the crew is unknown. The status of the ship is warp core offline, running on emergency power and auxiliary systems, structural integrity breaches and pretty much everything else is offline. The computer doesn’t know what caused the damage.
The Doctor asks for the bridge logs to be transferred and for the last one to be played. Captain Janeway is telling the crew to abandon ship. According to the computer, all the escape pods have been launched and there are no humanoid lifeforms onboard. The Doctor states in his personal log that his usefulness appears to have come to an end and is about to terminate his program when he hears a pounding on the door.
The pounding comes from B’Elanna, who forces the door open. She tells the Doctor that internal sensors were damaged during the attack; that’s the reason why the scans didn’t detect her. Two Kazon Predator-class warships surprised them and Janeway and B’Elanna remained onboard to see if they could fix a warp core breach, which they did. The escape pods were tractored onboard the Kazon ships, which then left.
The Doctor’s tricorders are not registering B’Elanna’s lifesigns and she tells him he needs to help the captain, who is on the bridge. The transporters and turbo lifts are down, so B’Elanna wants the Doctor to go to the bridge himself. It seems they have been installing holographic emitters on critical decks. They haven’t been tested yet. B’Elanna is heading to engineering and the Doctor appears on the bridge. He comments that it’s bigger than he thought.
The captain is unconscious and the tricorder – a different one – doesn’t show her lifesigns. He uses a hypospray to revive her and Janeway recounts what she remembers. B’Elanna contacts them from engineering; communications are up and she’s going to work on the warp core. The captain is going to work on the bridge controls. Then Neelix contacts them from the mess hall, asking for help; that is another location B’Elanna said there were holographic projectors.
In the mess hall, Neelix is defending himself against an armed Kazon by throwing food and cooking implements at him. It’s surprisingly effective. The Doctor distracts the Kazon and Neelix knocks him unconscious with a frying pan. Neelix looks to have been injured, but it’s just a tomato stain. He explains that Kes got away but the Kazon followed him. Then Neelix points out that the Doctor is bleeding. Neelix reassures the Doctor with the same words the Doctor used on him, but the Doctor is more concerned. He isn’t programmed to bleed. He contacts the captain to be transferred back to sickbay.
The Doctor is also feeling pain and the tricorder works fine on him, when it shouldn’t. The computer has never heard of the EMH program. When the Doctor says that it is running, he is told that no holographic systems exist in sickbay. The EMH program doesn’t exist either. The CMO of Voyager is Dr Lewis Zimmerman. The Doctor knows the name and has mentioned it before; it’s the name of the engineer who created the EMH program. Who the Doctor understands resembles him. But is supposed to be at Jupiter station. The Starfleet file shows that Zimmerman looks exactly like the Doctor, and the computer says he is the Doctor.
The captain and the others arrive and the Doctor explains the situation, how the tricorders recognise him as a real person but not them. Janeway says it’s probably a problem with the remote projectors, and says she will deactivate and reinitialise the Doctor. Ordering the EMH to deactivate does nothing. When the captain orders the computer to shut down all holographic systems, everyone but the Doctor vanishes.
The Doctor is now confused. He says something must be wrong. At which point Lt. Reginald Barclay, from TNG, appears and claims to be the Doctor’s assistant. Barclay claims that the Doctor is Zimmerman; Voyager is simply a holo sim running on Jupiter station. There was a problem with radiation and the program is malfunctioning. Zimmerman was running a program on the long-term effects of isolation on a crew comprised of Starfleet and Maquis. One which Zimmerman wrote. Then the radiation surge affected the computers.
Barclay is claiming that the Doctor is not the Doctor but Dr Zimmerman, and he’s dying unless the problem is fixed. He then attempts to convince the Doctor that he is real, not a hologram, causing the Doctor to become more than a little uncertain as to what is reality and what isn’t. That’s the sort of thing that can have lingering effects afterwards. (Of course, if this was a simulation, the series would come to a rather abrupt end at this point.)