R-Type/WMG

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!
 * It'd explain why Darius ships have massive Wave Motion Guns.

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.