The core organs, from a gameplay standpoints, are the twin taserlimbs, a solid-er core (which may or may not play the role of a brain, we do know it is vital), and a pouch filled with an acidic substance and where the core is protected -I would've guessed this would be a stomach, but the thoughts on tentacle hentai insinuate this might actually be a testicle. Yaaaaay. Or both, or a general internal cavity like an acid-filled peritoneum. The rest is gelatinous and, from a design purpose, undefined, so we can go wild on that side. All that matter is that it doesn't distract too much from the aforementioned organs, so that players can quickly identify what is important to try to deal with it.
Even the Hydrozers aren't fixed, since they have a generic attack. They don't even have to be related to the Polarizoa in any way, as symbionts/parasites can come from anywhere. Variants of them might be used as defenders of unrelated bosses, to represent a vast family of symbionts. Or they ARE related, and may be young of the species. The possibilities are endless!

Some additional thoughts on the beast's appearance:
- The Polarizoa is mentioned "penetrating" the submarine; this implies it has some way to inject its sperm, from the ability to form a temporary orifice to having a full-fledge piercing penis. (I take note of the fact that the first creature suggestion for the game is a rape-jellyfish. )
- To emphasize the extreme regenerative ability of the Polarizoa, the Hydrozers may be seen chewing their way through it with no harm done to their host.
- Since the Polarizoa "adhere it's tentacles to the submarine", it may have visible "fingers", suction cups, "jaws" or "claws" to facilitate prehension.
- It's unclear how much mobility the Polarizoa needs: does it drift and grasp submarines in reach or does it actively chase them, however slowly? Anyway, since it spends its fights attached to a submarine, one might expect speed not to be its forte. An additional constraint is that any swimming appendage shouldn't look like an additional weak point, and thus should be relatively inconspicuous. While the jellyfish bell is a perfectly viable way to go, a lot of small fins for a comb jelly effect could be cool-looking. Or perhaps the tentacles have deployable membranes and act as twin swimming tails until the Polarizoa reach its quarry, retract the membranes and grasp the submarine.

CommanderPro100 wrote:When the Polarizoa encounters the submarine, it believes it to be a female of its species.

This begs the question of what the female looks like. Admittedly, a blind jellyfish may not be very physiognomist, but that's an interesting starting point of reflexion. Clearly, the "boss" expects to encounter such a thing in the water treaded in-game, which implies that the submarine may very well encounter females -another creature to design. Conversely, once we have an idea of how the female looks like, we can take it as an inspiration to complete the male, exploiting the idea that they have some similarities.
Having clearly dissimilar male and female of a boss in the game might be useful. Perhaps the true danger of the female isn't herself, but the fact that males Polarizoas are attracted in her direction.

EDIT: I just realized that as it is described (indifferent to creatures smaller than itself, Hydrozers confined to a defensive function), the Polarizoa has no way to eat. Of course, giving the whole more reactivity would modify the core concept, so perhaps it can be handwaved as the fact that Polarizoa found at this depth are merely a reproductive form wholly dedicated to reproduction and unable to eat, like some butterflies are. More voracious stages are implied to exist deeper, out of reach of the submarine; they may rise to reproduce in order to escape predation.

Irontaco wrote:

Regalis wrote: Maybe some kind of pokedex-like thing where a new info page appears every time you encounter a new creature...?

Maybe the main computers in the captain room could have some sort of small wikipedia-ish hud with basic information on some creature's anatomy, with more info being unlocked the more you kill of them/the more you progress in the game. That way you'd have a basic idea on how to deal with each creature by inferring from anatomy info, with other entertaining facts and curiosities being unlocked later. ("Tiger Tresher Lore 4/10 Unlocked!")

I think a database makes sense in-universe (of course explorers would compile datas!) and could be used to emphasize the collaborative aspect of the game if for some reason it is only accessible in limited location. Imagine a poor diver trying to fight a boss while a few other players direct it by interpreting the database... and struggle to find the immediately relevant bits of data or disagree on the species encountered. !!FUN!! could be had.
On the other hand, a sense of mystery and, dare I say, dread would be cool too, so an encyclopedia shouldn't be too accessible.
I suggest a "library" room with computerized data, where common and harmless creatures would be as detailed as wanted, relatively common menaces less well described, and a whole host of relatively unique enemies completely unknown. Completing the database could then be done in various ways: a small progress at each encounter of the creature, a larger amount when killed, and the largest amount if the entity can be captured and properly studied. Additionally, some missions may be for research purpose: the crew goal would be given the beginning of a file on a rare creature, and would then be tasked with adding datas about this specific beast.

Absolutely love the idea and art!