Why do the habitats and vehicles refer to you as "Captain", even though most logs indicate that the Captain of the ship went down with it, perished in the crash, and the player is implied to be just a systems maintenance employee? Because, as the last surviving member of the Aurora's crew, the title of Captain is automatically handed down to you. (though also it seems the costs and collateral)
Why does the player character seem to survive Kharaa with less symptoms for longer than other humans have, such as the Degasi survivors? Because chances are you've been eating peepers all along! As the fish have some of the highest nutrients in-game, and are often used to disperse the cure throughout the ocean in order to keep the Kharaa under control, you've probably been more likely to eat peepers than any other fish — and keeping yourself healthy and alive in the process!
Similarly, this may be why Stalkers, which are described as highly intelligent, can be briefly subdued by offering them a fresh Peeper. They've noticed that eating Peepers keeps them healthy.
Why do all the lifeforms get Exactly What It Says on the Tin names? Because you're not a scientist, you're just a normal person! Of course you're naming things the first thing that came to mind.
The Artic Peeper entry in Below Zero implies that the scanner generates these names, with a note from the main character noting annoyance with some of these names.
The PDA entry for the scanner itself corroborates this point, saying the scanner will generate an easily memorable name if the target is not in the scanner's database.
Branding may also be involved in the PDA's name choices. It's an Alterra device, after all, and if the local lifeforms prove marketable in some way then the company would want easy-to-understand names that tell their customers what's on offer.
While the Sea Emperor's children might be able to stop the Kharaa on 4546B, the sea emperor species is doomed in the long run as there are only five individuals left who are all siblings meaning any mating would result in inbred offspring. Unless they can breed without the nasty side-effects or are capable of asexual reproduction.
They are, according to research done by the Precursors, all life on 4546B is asexual, and reproduces likewise. The Emperors can be recovered. Incidentally, the Kharaa may actually aid in asexual reproduction by introducing mutations. Huh.
Actually the PDA states that while all species on the planet have one gender, they still need to mate to reproduce.
Taken directly from the PDA entry on reproduction: "However in rare case only one parent was required, with evolutionary mutation introduced by the effects of the environment itself". I'm willing to bet that the Sea Emperor Leviathans meet that rare exception. And that most other leviathans do as well.
It's also possible that there are other, unrelated Sea Emperor eggs lying dormant in some obscure corner of the planet, too inert and impregnable for the bacterium to infest, but unable to hatch. Revival of the ecosystem will hopefully provide them with the stimuli necessary for natural hatching, or the five new Sea Emperors might seek them out and provide what's needed.
Not having firearms - or even directed energy weapons - in a game set primarily underwater makes a lot of sense the more you think about it. A laser would diffuse in water incredibly quickly and be mostly worthless. Any sort of traditional rifle or pistol would be worthless as the water drag slows them down to being harmless to a person within a few feet, let alone any monster you might run into. Never mind unless you had let water into the action, the gun would probably detonate in your hands. The only possible exception would be grenades for much the same reason albeit smaller that depth charges work (and even then, they'd only majorly harm things above them).
The game also mentions an unfortunate incident when weapons could be produced by fabricators. It is implied that a crew turned on its leadership in a time of crisis, so it makes sense that the Corporation banned civilians from fabricating weapons. At least one conversation comes up where an officer tries to lift the weapons ban when they crash land in a hostile environment where the weapons can be pointed outwards instead of inwards.
The Player Character might not be as screwed as you might think about that Trillion credit debt they found themselves in, if you played the game 100%, The PC might be able to trade the knowledge he gained while on 4546B, He knows what happened to the Aurora, he knows what happened to the Degasi family and where their bases were, and also he knows the location of every single bit of alien tech is, including a giant plasma cannon that can take down a starship,and batteries an power cells that are 20x more effective than what Alterra has, and a cure for a disease that is apparently very very bad, surely all that info would forgive something as simple as a debt.
Or, on Alterra's side, the debt could be used as a bargaining chip to secure the Player Character's cooperation. See The Trial of Ryley Robinson, a very nice fan short story.
It's also entirely possible, nay, probable, that a trillion credits just isn't all that much money. After all, we can manufacturer many gemstones in industrial quantities today, and only the artificially manipulated jewelry market keeps the price of those things high. There no reason to believe that such exorbitant prices will continue to be the norm, so Riley probably paid his debt out of his pocket change.
Ryley has just lived through an experience that would make for one of the most impressive Robinson Crusoe stories since the man himself. Selling the rights to his story would probably be enough to clear his debt to Alterra and live comfortably for the rest of his life into the bargain. Also, considering that the Kharaa seen in Natural Selection 2 are presumably causing a huge, huge problem to the Federation off-screen, the information on how to potentially CURE IT that Ryley has discovered might be quite literally priceless.
In Below Zero, Robin doesn't show any aversion to eating the fish of 4546B, despite the first game having mentioned that humans in the setting are used to eating synthetic foods and find animal meat disgusting. This is because Robin has been forced to survive on her own in hostile environments before as part of her missions for Xenoworx, so she's already desensitized to eating whatever food she can find in the wild.
However, this has been changed with a recent update, though it doesn't exactly decrease the fear factor. One lifepod is missing an entire half, one lifepod is still floating, but upside-down for some reason, and the rest have been relocated to other biomes. What do the biomes they were moved to all have in common? They are all filled with dangerous creatures.
According to the bits of story we have right now, those pods were damaged and the occupant taken/killed by something(s) that were hunting and gathering the Aurora survivors. You were lucky enough to escape detection.
Most were taken/killed by the Warpers. Artificial, cybernetic lifeforms built by the Precursors to help deal with the Kharaa infection by disposing of infected creatures. This in turn explains the similarities in the damages inflicted on the pods - the Warpers are basically bio-organic drones, so they all operate on the same logic patterns and therefore one will always dispatch their targets in the same ways as the others; by gouging out one of the occupant seats and killing whoever else is in the other. Furthermore, you can actually hear (read) communications between Warpers via your communication relay that describe their hunting the other crewmembers - and can do nothing to stop them, even when they transmit that they have detected 9 survivors....and then later transmit that only 1 survivor now remains: You.
One Lifepod landed relatively intact and wasn't in immediate danger from the local predators. There are no Warpers nearby. So what happened? Reading the PDA log reveals that the on-board fabricator was faulty, and screwing up everything requested of it. Observing the damage to the lifepod, you realize it's blown OUTWARDS...
Planet 4546B is ravaged by the Kharaa Bacterium, and the only source of Enzyme 42 is the Sea Emperor Leviathan. There is only one Sea Emperor Leviathan on the planet - at the location you crashed. That location also happens to have Peepers ensuring that the Enzyme escapes into the food chain, protecting the life forms there from horrible, bacterial death. What about the rest of the planet? Is everything else on 4546B dead and sterile due to the Kharaa, or is the Kharaa trapped within the crater?
Depending on how fast the Kharaa incubates and kills nonhuman victims, it could be that the bacterium created its own firebreak and 'only' wiped out all life in a fixed radius around the gameplay area. The upcoming Arctic DLC at least hints at life elsewhere on the planet that may have survived or avoided the Kharaa outbreak.
The Dead Zone is an empty black void surrounding the entire map of the game, populated by nothing but gigantic Ghost Leviathans to stop you from exiting the game area. While this is simply a gameplay mechanic, this might imply that the area where the Aurora crashed is the only part of the entire planet that isn't part of the Dead Zone. Are the Ghost Leviathans the primordial species of life in 4546B?
The playable map is the caldera of an ancient volcano. The Crash Region is the center of that caldera, and is raised from the sea floor by the volcanic activity below. That is also the reason for all the volcanic vents and activity, and is likely why the region has such high biodiversity - volcanoes are known for producing high-nutrient regions. It also means that the Aurora could easily have landed in the deep pits of the caldera, if not for luck & good aim.
The Crash Zone, the murky, desolate, irradiated region named for being the location of the crashed Aurora, may have very well been part of the safe shallows prior to the crash. The little fauna and flora in there matches that in the shallows, plus the area is littered with the exact same coral tubes. The Stalkers and Sand Sharks around the area may imply that it could have also included Kelp Forests or Grassy Plataeus.
In addition, the Crash Zone is infamous for being inhabited by 8 Reaper Leviathans. However, the only other places Reapers live (the Dunes and the Mountains) are on the other sides of the map, far away from the crash site. There is also no evidence that they migrated all the way over to the Aurora. Maybe the Safe Shallows weren't originally so safe...
There is a mini biome in the southern part of the Crash Zone informally known as the Crash Zone Mesas. This may be the only remains of an entire biome that was destroyed by the Aurora crash. Possibly one that was home to Reapers.
One user on the official Subnautica forums pointed out that although you're cured at the end, any other organisms or substances you knowingly (pet cuddlefish) or unknowingly (detritus) take with you off 4546B back to Alterra space may be carrying Kharaa bacteria, or even that you, while cured, have become an asymptomatic carrier. Have fun being the instigator of an intergalactic pandemic!
The players home civilization doesn't exactly seem like the nicest or most stable place to live. They literally have contracts for relationships and other social functions. Doesn't help that the player is on the hook for paying off a HUGE debt for all the minerals they used up on 4546B which the Alterra corporation automatically claimed ownership of even if they survive.
Note that the PDA never instructs Ryley to do anything to aid his survival - build a campfire or tent on the islands, weave a net, make a fishing rod - that he might potentially pull off without additional Alterra technology. Was it specifically designed to ensure anyone surviving as a castaway would be left as indebted to Alterra as possible, both emotionally and financially? Also, have human beings become so tech-dependent that even the idea of such improvisation never so much as crosses Ryley's mind?
it is heavily implied that this game takes place in the same universe as Natural Selection 2. In that game the Kharaa turned people into monsters along the lines of Necromorphs. If it really is a case of them not just reusing the name, then that implies that there's variants of the disease out there in the universe that are just as deadly if not more so. Just what the hell were the Almanacs up to?
The Warpers killing and carrying off the infected to be (presumably) disintegrated makes a horrifying sense in that context - they're disposing of the dead and dying before they transform. Imagine if Enzyme 42 didn't exist and the Almanacs had failed to contain the pandemic: the entire planet would've eventually become another colony for the Kharaa as a species.
Speaking of Warpers, consider their very existence: they were designed, built and programmed to be hunter-killer-protectors the fauna of the planet grows to hate. Their, as it turns out, flawed creators (basic understanding of non-cybernetic mental communication, motherhood and egg hatching not a specialty, so who knows what else they're blind to) left them to function on automatic for thousands of years without any biological needs deemed superfluous to their designated function. They are intelligent enough to communicate "verbally" with each other using techno-telepathy/ radio/ whatever. They cannot age, but they can be killed. They cannot change as individuals or as a "species" when the situation around does. They cannot reproduce, although they seem capable of mending themselves somewhere. They are outside and to one side of being alive by any biological metric. If they're even remotely sapient (which they could well be), this is And I Must Scream distilled. If their biological, behavioural and cybernetic programming even allows them to scream, that is.
The game features three specialized deep sea vehicles with defined, upgradable crush depths - go deeper than allowed and they'll be destroyed in about ten seconds. The Player Character himself only wears a diving suit without any additional protection, yet he can dive as deep as he wants without problems aside from increased oxygen consumption, and that can be countered with a simple rebreather item. The water pressure is about to crush your nifty Cyclops sub like an empty beverage can? Just bail out, it won't do anything to you. Nowhere is it ever explained or even mentioned how that's supposed to work. It could be intended as an Anti-Frustration Feature, but seeing how realistically the game treats your fight for survival otherwise, it wouldn't have made much of a difference to let you die in case your vehicle gets destroyed too far down. Instead it just comes across as immersion-breaking.
Except this is actually Truth in Television - well, sort of. The human body is pretty incompressible (being mostly water, after all), what would actually kill you is the gas in your lungs and bloodstream expanding due to the rapid pressure change your body would experience stepping out of the submarine. You can actually go pretty deep in real life with the right preparation - the current record is ~300m, but much deeper is theoretically possible if a liquid air substitute is used. The only issue is that we're never shown the player character using such equipment, but it's entirely possible that Alterra figured out how to solve the issue with Nanites or some other future tech - which would also explain why our character doesn't experience the bends.
The Aurora was on a mission with the possibility of a water landing. It's possible (part of) her crew was specially modified to be semi-aquatic or that the crew already had such mods due to the Aurora being an aquatic-mission ship.
It's not a normal dive suit, it's what the game calls an AEP suit which the data bank points out is designed to withstand pretty much everything the universe can throw at it. Heat and cold are likely a problem because they transfer through the suits material, but since it's "a hermetically-sealed personal environment" pressure is a non-issue baring going deep enough to actually destroy the suit itself. While 1500m is deep we can assume the AEP gives you pressure resistance comparable to a submarine most of which can hit 2000m without issue and some can go as far down as 10,000m. The Subnautica vessels are actually pretty pathetic in their dive depth. More mystifying in this case is the fact you can get chomped on by critters without the bites causing an instantly fatal breach when you're at 300m+ down.
Perhaps the suit has a backup micro-version of the stasis gun like Star Trek forcefields.
The real question is how the base suit protects you from pressure when it doesn't have gloves or a helmet.