The exact origin of the Borg is a source of great mystery and of speculation of non-canon authors. These accounts, as outlined on Memory Beta, are largely contradictory.
Intelligence provided by Erika Hernandez during in the Borg Invasion of 2381 suggest the Borg have a definite point of origin from a crashed and temporally-displaced Caeliar cityship, Mantilis, in 4527 BC. However there has also been evidence of Borg activity much earlier, such as the assimilation of the Hirogen homeworld around 110,000 BC, and possible Borg-Preserver conflicts dating back to billions of years ago.
All we do know in canon, is that the Borg have existed as a blend of the biological and the technological for “thousands of centuries”, as Guinan put it (“Q Who” [TNG]). Taking into consideration these contradictory accounts of the origin of the Borg, one can assume that various iterations assimilated one another to become the Borg Collective that spans the Delta and Beta Quadrants of the Milky Way galaxy.
There’s also the matter of why the Borg Queen is traditionally a member of Species 125. Why not Species 1? Furthermore, the version of the Borg Queen played by Susanna Thompson in the Voyager two-part episodes “Dark Frontier” and “Unimatrix Zero” claimed to have been assimilated as a child roughly a decade earlier. One possibility is that Species 1 through 124 belonged to one of those earlier separate iterations of the collective. Additionally, “The Origin of the Borg” segment of the Star Trek: Legacy video game suggests that in their quest to achieve perfection, the Borg discovered that the females of Species 125, “displayed a mental prowess, enabling them to sift through thousands of thoughts and bring order to chaos.”
Certain aspects of the Borg are perceived as continuity errors. For one, the whole concept of a Borg Queen completely contradicts the idea of a collective consciousness. When you think about it, how is it that the Borg Collective is always in a state of consensus? The possible explanation is that each individual Borg is merely a drone subservient to the will of the Queen just like the hierarchy of an insect colony. That arrangement adheres to the TNG producers’ original plans for the Borg to be an insectoid race when the final episode of the first season was originally intended to introduce the Borg—with the events of “Conspiracy” serving as a precursor episode. The Queen is the one who brings order to chaos. If a single drone has any inklings of embracing their individuality and who they were prior to assimilation, the Queen swoops in and puts a stop to it. As the Queen put it in First Contact, “I am one and many.” In response the question of whether or not she was the leader, she said, “I am the Collective”–an answer Data found “interesting, if cryptic”.
Haters of Enterprise have pointed out that the Borg did not use their traditional greeting—“We are the Borg. You will be assimilated. Resistance is futile”—in “Regeneration” In fact, for some technological reason, the first sentence of their so-called “traditional greeting” was not heard. This complaint is based on the expression that “haters gotta hate” since the Borg have not always used this greeting. Others have included:
“We are the Borg. Lower your shields and surrender your ships. We will add your biological and technological distinctiveness to our own. Your culture will adapt to service us. Resistance is futile.” (Star Trek: First Contact)
“We are the Borg. Existence as you know it is over. We will add your biological and technological distinctiveness to our own. Your culture will adapt to service us. Resistance is futile.” (“Scorpion, Part I [VOY])
“We have analyzed your defensive capabilities as unable to withstand us. If you defend yourselves, you will be punished.” (“Q Who” [TNG])
Wait a minute. Nothing about assimilation?
Even with the information Guinan provided about the Borg, as far as Starfleet was concerned, assimilation did not appear to be part of their plans for galactic domination. “The Best of Both Worlds” was the first episode to introduce assimilation as part of the Borg’s strategy to attain perfection.
Shelby: I thought the Borg weren’t interested in human lifeforms, only our technology.
Picard: Their priorities seem to have changed.
This “change in priorities” was never addressed in future episodes or movies. In fact, possibly because the events of “Regeneration” were not public knowledge or had not happened in that timeline, Magnus and Erin Hansen (Seven of Nine’s human parents) were the first humans the Borg assimilated in 2356. (“Scorpion, Part II”, “The Gift”, “Dark Frontier [VOY]). One possibility is that, at some point in their history, the Borg Collective decided that assimilation of humanoids was more efficient than procreation. Perhaps the Borg cube the Enterprise-D encountered in 2365, for whatever reason, was following some older programming directives. The away team’s visit to the “Borg nursery” would seem to contradict Seven of Nine’s statement that the Borg have no need for procreation (“Revulsion [VOY]). Perhaps Commander Riker’s conclusion that the Borg were born a purely biological lifeform was incorrect and the infant Borg were assimilated infants. Or they were a branch of the collective that still procreated rather than assimilated.
The idea of multiple branches was suggested in the Shatner-verse novel “The Return“. Captain Picard is certain the Borg have been defeated after the events of “Descent, Part II”. Commander Shelby counters that he and his crew only defeated one branch among many. Each of these branches may have its own queen with the exact same agenda, all of whom fall in line with an “uber-queen” (Stargate: Atlantis character Rodney McKay’s description of the Wraith Queen known as the Primary).
In spite of the Borg having been completely eradicated in the 2008 Star Trek Destiny novel trilogy, they are still a source of intrigue for fan-fiction writers and creators of other non-canon media. In fact, the Borg are still a major threat in the Star Trek Online universe. But as Pocket Books author Christopher Bennett suggested in a TrekBBS forum discussion, the writers backed themselves into a corner by creating this nearly invincible enemy. They were featured fairly infrequently in The Next Generation, only to be “ruined”, as many fans often complain, by their more frequent appearances on Voyager.