Maybe this has been brought up before but it's bugged me since I saw this episode. Why did The Doctor delete the Equinox EMH instead of merely deactivating him. Seems to me that they could have done so to the same effect and while he/it was offline restored the ethics programming the absence of which turned him into a holographic Mengele. Then Voyager would have had the back-up EMH they always said they wanted.
From a deactivated the state the Doctor, "an" EMH can reactivate himself into working order. The Doctor acts irrationally to make his patients feel at ease, a function of his personality which he cannot turn off, otherwise he wouldn't be solving voyagers woes at human speeds and otherhuman limitations.
The Doctor could have shrunk his holographic matrix like in.. I think it was the Cloud where he was shrinking. Then he could call him Mini Me. This is a terrible missed oppurtunity.
Voyager's EMH was the only one with the ability to turn himself on and off. I suppose with the Equinox programme transferred to Voyager he would have the same ability, but I doubt he would know about it, seeing as it was a unique feature. As for why he deleted the "evil twin", well, it wouldn't do to have a duplicate when it came to all the crap about holographic rights, proving that holograms are mass-manufactured, programmable tools.
He wasn't huge? He was being projected into space by the same parabolic mirrors that were projecting the fake starships, which were huge... But it has been a while and my memory makes fun of me for sport.
But that argument only applies if the original images of the ships were small and they were using the mirrors to enlarge them. Being parabolic, it would seem to me that the mirrors were being used to focus the images and project them into space, not enlarge them. After all, wouldn't that be like enlarging a picture in photoshop? Sure, it gets larger, but it also gets more pixelated. I can just imagine the Kazon saying, "No, those Talaxian ships are fake! I can tell by the pixels!"
Well he appears to be regular sized, although I would have assumed that the disrupter beam used by the kazon would be much larger compared a human being sized mass. Depending on the focal length, where you're making the hologram "appear" would indicate the size of the holograms., and since they wanted a huge ship, it would be odd that a regular sized doctor would come up out the other side of holographic manifestation that was supposed to be the size of a starship... Oh. His ego. Got it.
They'd have had a backup EMH program. They wouldn't have had the DOCTOR - his life experiences, the things he'd learned about how to get along with people, in essence, his personality. And who knows how much damage the Equinox EMH went through besides his ethical subroutines being deactivated? They would have to completely delete all his memories of ever having done evil things, or he'd never be able to function - nor would anybody ever be able to trust him.
According to swarm in season 2 and season 4's message in a bottle they didn't have jack shit. 7 episodes after message in a bottle, we see an episode set an unknown number of months or years into the future were they had a working backup. Originally he couldn't even go to the holodecks. They didn't say that he couldn't, but they said he was stuck in sick bay forever until heroes and demons which they made out was his first time out of sick bay even they they had been in the delta Quadrant for months.
The writers completely ignored the existance of the Equinox officers after the two parter was done. They aren't known for paying attention to things that happened in previous episodes! Also what ever happened to the Borg baby?