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In Star Trek: Voyager, episode 23 of season 4 (remember), the episode begins with a civilization unknown until now. They claim to hold the ruins of the USS Voyager, which has otherwise contributed to the history of this civilization in a negative way, whereby Captain Janeway formed an alliance with the enemies of the people in question.

In the historical reconstructions of this event, we see many parts belonging to the ship, such as the Doctor.

This one -- having been deactivated during all these years -- still seems to be several centuries ago. The Doctor is therefore considered as the last "living" witnesses of this war.

The USS Voyager was considered a heavily armed warship with a restless and violent crew. The Doctor has done everything to set the truth about that time, and finally, all ends well, history is approved.

However, what is really going on? In the other episodes, the Doctor is always present, as well as the crew members, and the USS Voyager. At the end of the series, they all return to Earth.

What about this episode that seems to be out of the scope of the story?

I couldn't find any explanation about this episode, except that we could consider it as a separate story, but it doesn't really make sense to put an episode that has nothing to do with it in the middle of the series (even if it's very good and fits in pretty well).

I don't think this question is a duplication of this post, because this one is about the whole episode, as well as what really happened to the crew.

Lets look at the transcript.

The Kyrians did not find a wreck of Voyager. They found a few relics and a partial blueprint:

EMH: Evidence? What evidence? Like this, for example? Triple-armoured hull? Thirty torpedo tubes? Twenty five phaser banks? This isn't what our ship looked like.
QUARREN: We reconstructed it from a partial schematic found in the Cyrik ocean, which was badly damaged by corrosion. We were bound to get a few details wrong.

In fact, they had very little physical evidence, as an earlier conversation shows:

QUARREN: Take a closer look. The evidence is all around you.
VASKAN VISITOR: Some musty fossils and a recreation? That doesn't prove anything.

Even a bit before that, we hear this little gem:

QUARREN: We believe they had a complement of over three hundred soldiers.

Three hundred soldier would be twice as much as Voyagers whole crew complement. Suffice to say, if they had found a wreck, they would have more accurate numbers.

We do learn a little bit how they got into possession of some of the artifacts:

EMH: That's the EMH backup module. One of your attack parties must have taken it from Sickbay.

Later, we see the Doctors account how Voyager was boarded with those attack parties.

In summary, Voyager was not destroyed. They took some pieces during the attack on Voyager. Some were lost and later re-discovered. They only had partial information, a partial plan of Voyager and constructed a narrative that fit with their world view.

I thought they only found a EMH backup module of the doctor. Like it says in the the post you linked to.

Since it is a backup the real one is still on board of the "real" Voyager as is the whole crew. So I think in the end the backup Doctor returned to Earth over 700 years after the return of the real voyager probably even meeting the real one.

Besides they just found some pieces of Voyager that gave them the room to the assumption that Voyager was a bad ass war ship with how many was it? 20 Phase Cannons?

We will never know.

That's the thing with history — it's all an interpretation, told through someone else's hazy memories. Be it the Kyrians with their politicised and time-ravaged storytelling, or the backup EMH who we can generally understand to be truthful but is still just one person with one person's point of view.

Arguably, this interesting facet of life was the entire point of that story, and that story is made all the stronger by the fact that we are never shown first-hand the events of that period.

(One could argue that we are supposed to take the backup EMH's holodeck recreation at face value, but he himself admitted in dialogue that he had to extrapolate in a few places, so y'know.)

What we do know, however, is that neither the "original" EMH nor Voyager herself were ever left behind on Kyria (and the episode doesn't claim otherwise; you've misremembered it). That's why we continue to see both entities throughout the remainder of the series. The parts of Voyager that you see in the episode were recreations on a futuristic holodeck.

1st most likely possibility: It stands to reason that this was an alternate universe and version of Voyager that didn't reach the Alpha Quadrant. Mirror-Mirror was one of the Original STs episodes that carried over to ST DS9, ST Discovery, ST TNG, and Enterprise but not "apparently" to Voyager.

2nd possibility: There was an Episode (Ep. 37, Deadlock) in which Voyager travels through a spacial Rift, thereby creating a second Voyager, with an identical crew, that later self destructs to save it's twin Voyager from a Vidian attack. They may have unwittingly went through another Rift and created a third Voyager on a separate occasion without ever noticing it (as in Deadlock Capt Janeway and Torres only realize there was another voyager due to a power drain during the Vidian attack, after Kes steps onto the other ship mistakenly).