The path to Anti-space and then Wherever in R-Type Final, the Hidden Ending that ultimately brings you to 2501, is in fact the best ending for the Bydo conflict. In this path, the protagonist will somehow find their way to a past/future, where they encounter and destroy the prototype weapon that would have become the First Bydo. This results in a massive temporal paradox, the shockwave of which affecting all possible futures where the Bydo exist. As the protagonist tries to outrun the paradox shockwave, the Bydo forces from multiple futures send everything they have at them in a final act of spite - Multiple instances of originally unique bosses, massive formations of Bydo fighters of all denominations, and finally, the last wave is a desperate last effort where the Bydo, having depleted their forces to drag the protagonist down with them, throw one last wave of corrupted training drones at the protagonist. You only get one chance to survive this gauntlet because if you fail, you will be dragged into the paradox phenomenon and be unmade alongside the Bydo.
The final stage of Delta, which takes place in the Bydo dimension, is filled with various distorted bits of human civilization and scientific knowledge, as well as crystalline embryos, while the Bydo Core takes the form of an ovum. While this can be interpreted as the Bydo spitefully mocking humanity for creating them, it can also be seen as a paradoxical longing to become their creators, a motif which recurs throughout the series in various forms (including the infamously suggestive Bydo Abyss in Final). Their very nature, however, makes the very notion of creating something new that isn't designed for more destruction all the more out of reach due to Creative Sterility. It's no wonder, then, why for all their hatred against all non-Bydo life, destroying and/or absorbing mankind is such an obsession.
Not unlike a certain Allied Mastercomputer/AM, the Bydo are strongly implied as not only being unable to fully escape their original "programming" by 26th century humanity as an interstellar weapon of extermination, but that they're painfullyaware of it. No matter how much they've evolved, killed or assimilated, the realization that they're still doing what they were made to do, and are fundamentally incapable of ever being like their creators is bound to have driven their collective consciousness insane over the millennia, further fueling their fathomless contempt.
While the DLC levels of Final 2 could be handwaved as fanservice, the game's conceit of being an in-universe effort by the Space Corps to document the war against the Bydo means that these could be seen as how the events of previous titles (including those retconned into the setting) actually played out. Given how Final previously established that human ships utilize sturdy flight data recorders, it's entirely possible to recreate battles set even in mind-breaking alternate dimensions that otherwise would be too incredible to believe, or impossible to perceive. Alternatively, they could be seen as simulations for training and future analysis, which may also explain the differences in said levels compared to their original versions (like having two Moritz-Gs or different variations of familiar bosses in locations where they didn't exist).
The Bydo. They are essentially the embodiment of the most evil elements of mankind and run off of mankind's most basic instincts. And they're Always Chaotic Evil, being completely incapable of being redeemed or even reasoned with. And that's not even mentioning its properties: they exist in a flux between matter and energy and can turn into a wave form. This means they can turn into a wave, bypass pretty much any form of protection, turn back into matter and begin The Corruption. In the second ending of Final, you get corrupted and fight against your former allies without realizing that you've been corrupted by the Bydo.
That's not even the worst of it. How did these horrible beings come into existence? 26th century mankind deliberately built them that way, to serve as biological weapons against other solar systems (the Bydo became Phlebotinum Rebels and humanity was forced to blast them into Another Dimension to keep from getting wiped out). This brings up two possibilities: 1. Future humanity was fighting an enemy so unbelievably horrific that the Bydo were seen as an acceptable weapon to use against them, or 2. Future humanity was bent on wiping out other species with the Bydo, which would seem to indicate that they haven't much left in the way of morals themselves...
R-Type Command II shows the Bydo waging interstellar war against a mysterious "Other Civilization", which may or may not be what the Bydo were originally created to fight. The Bydo manage to advance all the way to their home planet, but inexplicably leave it untouched and reverse course back towards humans. One fan theory is that the Bydo encountered something there that freaked even them the fuck out. That is saying something big as the Bydo are nearly legendary for their persistence.
There's another possibility regarding that. The suspiciously un-alien architecture and ship design style of the Other Civilizations combined with that spacetime anomaly you have to fight through on your way out pave the likelihood of of a second time-loop for the creation of the Bydo - or the first loop as the case may be. We've seen the Bydo turn around the way they do explicitly once before; the final moments of the first Tactics/Command. An enemy so horrific that future Humanity would create the Bydo in response? Who else but Mankind's own designs?
The fact that Final 2 exists suggest that the attempt to exterminate the Bydo once and for all in Final may have been All for Nothing.
Fortunately, this doesn't seem to be the case: Final 2's story is set up as a pilot running through simulations of past missions against the Bydo to try to glean new understanding and aid in weapons development, which suggests the Bydo have already been annihilated.
As revealed in Final and Final 2, mankind's eventually forced to incorporate and reverse-engineer Bydo samples to at least some degree into the ships themselves to gain an upper hand in the war effort, beginning with the aptly named RX-12 Cross The Rubicon. Not only does this result in murky experiments into using the enemies' own weapons against them, but it also leads into outright engineering Bydo-type ships, some of which are organic-looking monstrosities that are barely controllable. It's not much of a stretch to see how, even though humanity wins in the end, such "research" would in time lead to the creationof those very enemies to begin with.
. Not only does this result in murky experiments into using the enemies' own weapons against them, but it also leads into outright engineering Bydo-type ships, some of which are organic-looking monstrosities that are barely controllable. It's not much of a stretch to see how, even though humanity wins in the end, such "research" would in time lead to the creation of those very enemies to begin with.