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This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
The "multiple endings" in R-Type Final are actually distributed bits of a single story.
The endings all occur, in the order of Ending C -> Ending A -> Ending B, where Ending C is an attempt at reaching the Bydo source before it can evolve to become so damn insidious (which ends at stage 6.0, prelude to Ending A), and Ending A's tumble into the Bydo abyss ends at stage 6.1 (the prelude to Ending B). The player's Bydo-fied ship is then stored for research, and eventually used as the template for this new bioweapon that couldn't possibly turn out the way it did in the timeline the Bydo came from...

The Darius series takes place in the far future of the R-Type Universe.
Notice how, in the Bydo Dimension, the couple seem to become a fish midway into the level. This is symbolic of the ultimate in Bydo evolution. While they seemed to be dead, in truth the Bydo were simply biding their time, as usual, and evolving further. And when they returned... WARNING a huge battle ship is approaching fast!

You systems become weaker after being infected by the bydo.
Considering that you killed the last bydo as well, its source of hatred is not strong enough to destroy ships in one hit. Rather, it uses the Hot-Blooded determination to prolong the newly christened ship.

The Bydo are the real heroes, and they're doing everything in their power to prevent their own creation.
While, for the most part, we view R-Type from the perspective of a pilot giving his life to protect humanity, there's lots of material to suggest that humanity in R-Type is the biggest bunch of jerks in the universe. When the Bydo aren't around, we get busy slaughtering each other wholesale, and ultimately we create the Bydo, which are about as bad as every sci fi nightmare species combined and THEN some, because just being able to blow up planets wasn't enough for us anymore. We do this for the sake of efficiently committing genocide against our enemies. It's heavily suggested that the Bydo were created by perverting and corrupting human DNA to the absolute maximum until we'd stripped out the humanity and left it only able to expand and consume and hate. We consigned them to another dimension, and they did the only thing they could do: They converted everything to Bydo. We don't even know what was in that dimension before, but it sure isn't there now. It's the most extreme form of dumping toxic waste in the wilderness possible.

So when the Bydo finally break out, they come after us in a time period before we created them. We don't really know how time travel works in this universe, but as of R-Type final, it's at least assumed that making changes to the timeline will affect this timeline, so if the Bydo care about their own existence at all, what they're doing doesn't make sense. Furthermore, they know the future, and they still throw everything they have at you to keep you from getting there, where your force unit becomes the basis for their existence.

Then there's the imagery; remember, the Bydo define every aspect of Bydo space, so what we see there is all displayed intentionally. In the final level of Delta, the Bydo bombard us with images of human progress, the ultimate result being an organic area comprised of more obvious Bydo forms. The "standard" final level of Final has them showing us two humans having sex at different angles. I think all of this imagery is an attempt to communicate with us exactly what they are, and possibly a warning or a plea.

Nothing about their existence seems pleasant. They're like a cancer that can't stop growing aimlessly and metastasizing. It's suggested that they have an instinct for destruction, but that doesn't mean they aren't intelligent (they eat human thoughts, after all). I think they hate themselves as much as they hate us, and are desperately trying to commit suicide the only way they can - by preventing their own creation. We just keep stopping them, and continuing to be destructive, genocidal jerks all on our own.

The reason the Bydo where considered a viable weapon in the future where cause of a Evil Versus Oblivion scenario.

Rose & CamelliaWMG/Video GamesRune Factory

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