In Star Trek, the Borg Queen is said to be from Species 125.
Has this species been identified? Or has it been assimilated before the rest of the galaxy could encounter them?
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Here is my guess about species 125.
The Queen probably didn't exist until species 125 was assimilated, but given what is stated in Star Trek Legacy (they don't identify them as species 125, but it's pretty clear that they are 125) they were assimilated into the collective to give the Borg more extended control due to their mental abilities of only the females. From the sounds of it all of species 125 was assimilated, and they might have been what formed the collective how it is in the story today.
Now for the guess:
Now the Borg Queen is seen as a single entity, but apparently all of species 125 that is shown in the game all are female (or more to the point the Borg were only interested in them because they had the mental abilities the Borg desired). Given the look of the women in that scene all look like the Borg Queen without the cybernetic implants. the females of species 125 look pretty much identical, so the Borg Queen might be an entity created by the collective that (again guessing!) is a polar opposite of the collective, the Queen is an individual with countless bodies. It also could in canon explain how she can be destroyed in two different places (or time lines) and still exist. It also makes a good argument why she is the only one seen as species 125. (Also makes the Borg a lot harder of an enemy to destroy if the Queen exists in multiple bodies in multiple locations, all of which share one mind and one will)
Anyway that's my theory on species 125, it's not canon though! But it could be if they go that route with the Borg's history.
No members of Species 125 have been encountered outside of the Collective.
I came away from "Dark Frontier" with the impression that most, if not all of the species had been assimilated, but I can't remember if that was ever stated directly.
The Caeliar could be species 125. The reason they were just assimilated and had been known before was because the Caeliar were sent back hundreds of years in time because of an unstable star system caused by their imprisonment of federation crew memebers. They were in a massive city ship that was sent back to the Earth year 1500ish something. It is part of how the Borg were created. In theory the feed back pulse that caused the star to go on the fritz could have been The Q's dealings. The Caeliar liked to control things and use very advanced technology.