Just before you fight O.V.U.M, you see a red image in the background before the background changes. That is Bacterion in his "Giygas" form. After the background changes, 3 Intruders (the dragon boss from Salamander) fly from the background into the foreground to form Zelos, which change into Brain Golem, which changes into a small sphere that can be destroyed. So Bacterion materialized himself to battle you, which didn't work.
The temporal space fighter is simply equipped with some sort of proximity-triggered failsafe that warps it away to a previous safe spot before it is destroyed or serious damage is done, the trade-off being a high energy cost (lives and power-ups). This would explain the Vic viper's memetically fragile nature, as well as why the explosion looks like the ship zapped out of existence.
Every time a leader is defeated, it's scattered pieces seek each other out in order to battle and consume each other, escalating in power and intelligence from simple "prey-or-predator" nature to off-screen cosmic battles to build strength and establish dominance. The one that comes out on top has already assimilated the others, and become a dominant intelligence which will go on to assault Gradius. For this reason, it is unlikely that two or more Bacterion leaders will emerge at the same time, unless a remnant comes into contact with some other powerful or intelligent life-form (possibly leading to the events of Salamander), which more or less assimilates the bacterions.
- Gofer suggests otherwise in Gradius IV. However, because this is his first chronological assault on Gradius (Gradius II wouldn't occur until many generations later), it's possible he didn't realize or anticipate the behavior of his own cell structure.
Let's face it, how does one explain all the crazy shit you can pull off with those Options, especially in the opening cutscene of V?The pilots possess exceptional reflexes in order to survive their treks, the Options are the Bit/Funnel equivalent for the ships, and the original Vic Viper pilot, James Burton, and its designer, Dr. Venom, possessed ESP (similar to Newtypes); thus giving them a method to use the Options the way they do. This carried on to James' descendent, David, who also possessed ESP, survived his mission, and did crazy stuff with his ship's Options. Any other pilot would have had to been enhanced, akin to creating Cyber-Newtypes; hence, how Lord British and the rest of the pilots can use their Options and have lightning-quick reflexes.
It would explain why said boss shoots rings that can be shot away, and why V does not have a moai stage.
- JOSSED! Moais still exist in NEO, but V avoided this by not going to vandalize them.
In a version of events where the Northern Cross War did not occur, Dr. Venom was arbitrarily attempting to play God and create some form of lab-grown life, only to scrap it when he assumed it to be a failure. When it eventually attacked Gradius, he realized its true nature, and used this to his advantage during the events of MSX Gradius 2 and beyond, essentially making him The Man Behind the Man all the way up to Gradius V, set conveniently at the end of the series timeline, before the Bacterion threat is officially declared over. In the Northern Cross War timeline created during Gofer No Yabou Episode II, The Bacterion will themselves into existence, and still respond to Dr. Venom when his coup fails.
Since Gradius V is set in the same millennium as Gradius NEO (both set thousands of years after previous Gradius games) It would be safe to assume that the Gradian Empire doesn't even exist anymore prior to the events of Gradius V. Also, the Lars Empire is behind the Bacterians who was destroyed in Gradius V.
Alternatively it also describes your player skills: You're merely a legend if you can beat the first two Gradius games, but if you can beat the third, you deserve to be in a pantheon of some sort.
The entire Parodius series is just a ploy to get Penta into the Gradius universe so he can destroy the Bacterian by running really fast through them.
This also explains its tiny hitbox in some games - damage to the ship's wings can be safely ignored because the recombinator can simply restore peripheral systems and hull plating on the fly, and only hits straight to the main reactor/cockpit will have any permanent effect.