I've sometimes seen this sentiment, especially among reviewers, that SOMA's WAU ""monster plot"" contributes nothing to the main game's story, and that the storyline would infact benefit from the WAU's removal. If you ask me, that couldn't be further from the truth. The WAU is at the root of everything. Frankly, it's the main reason the game's moral dilemmas are.. well, dilemmas at all. If the WAU wasn't making monsters, wasn't there to warp the life around Pathos-II as it saw fit, the game wouldn't have even started. Pathos-II would've just remained dormant forever. Simon wouldn't be there, and neither would any of the obstacles he faces on his journey to preserve humanity. The main reason the WAU isn't directly beneficial to Earth is exactly because its understanding of "life" is so skewed. Its not just bringing things back - its bringing them back incorrectly. Every single "monster" we meet builds a case both against and for the WAU's continued existence.
The Construct shows the WAU's failure to understand humanity in the physical sense, shoving a Human brain scan into a misshapen robot body and calling it a day, leaving it to babble to itself as it aimlessly wanders the halls of Upsilon.
The same could be said for Carl Semken and the other Mockingbirds, though to a lesser degree - though capable of speech, they're still very delusional and oftentimes end up going insane. Still, in some ways you see the WAU's understanding of human psychology progress with each new mockingbird - they become increasingly coherent and increasingly sane, Catherine and Robin Bass being great examples. While the Construct has lost so much of itself you can no longer tell who it used to be, the other Mockingbirds have their sense of self intact.
With the WAU's unreliable nature cemented, we move on to its attempts at preserving humans physically, with Amy Azarro being the first proper example Simon gets to witness.
She's kept alive in what seems to be a perpetual state of discomfort, and judging by the structure gel slowly overtaking her I believe the WAU may be slowly converting her into one of the Fleshers. Its keeping her alive, yes, but its doing so at any cost necessary - it doesn't matter if she's in constant pain as long as she doesn't flatline. Its treatment of actual organisms is practically an inversion of its treatment of the Mockingbirds - instead of prioritizing the mental wellbeing of the subject, the WAU prioritizes their physical wellbeing with little to no care for the mental state its "patient" is in the entire time.
Fleshers live and breathe, but they seemingly aren't "all there" at all. The lights are on, but no one's home anymore. All they do is wander the ruins of the CURIE and lash out at anyone who enters their territory - the WAU has basically reduced them to animals.
Terry's been driven insane from all the structure gel infesting his insides, and though his goal was "technically" benevolent (putting everyone into a permanent dream state where the WAU could make them live the best possible versions of their lives), he achieved it through incredibly violent means, conducting what was basically an attack on Theta and causing its downfall. So far, its attempts at preserving humans physically have simply resulted in increasingly grotesque and violent monstrosities - but I would argue you see that begin to change when Simon reaches Omicron.
When you reach it, you see the aftermath of a particularly gruesome procedure WAU had carried out - everyone's blackboxes have exploded, turning their heads to mush. We find out that one of the employees, with the help of someone particularly close to the WAU, had figured out how to poison it. They have been receiving "visions" and "messages" from a comatose Johan Ross - the WAU's "AI psychologist", someone it desperately tried to restore from a comatose state by manipulating structure gel with electromagnetic fields. Either the WAU deliberately retaliated when it figured out the poisoning plot, or it had simply overdone it when restoring Johan Ross - sacrificing an entire station's worth of lives to bring someone back. Either way this shows a tremendous amount of intelligence on the WAU's part - and also paints it as either exceptionally cruel or exceptionally empathetic depending on the perspective you view it from. Either it considered Johan so important to it that it was willing to sacrifice most Omicron staff, or it was willing to violently retaliate in order to preserve itself.
Either way, Omicron houses what I believe to be a sign of the WAU's steadily improving understanding of humanity - Dr. Johan Ross.
He has been restored with both his physical health and mental faculties (relatively) intact. He isn't violent, and he perfectly understands what condition he is currently in - but despite that he doesn't seem to be physically suffering. He is still driven to eliminate the WAU, but it seems to be less out of personal suffering and more out of fear in regards to the suffering its other creations may go through. I believe he's an example of a semi-perfectly restored human - both him and Simon himself. They're both cases of, as Catherine puts it, "a sound mind in a sound body". But although the signs are there, there is no outright definitive proof that the WAU's creations will only continue to get better.
And that's what makes the game's final moral dilemma so compelling to me. The whole game has been providing us with both evidence and counterevidence towards the WAU's idea of restoring humanity. Now, it's up to you to act as its jury and executioner. By killing it you either stop it from torturing the memory of humanity, or you doom humanity to extinction in all senses of the word. By keeping it alive, you either doom the remnants of humanity to an eternal torturous existence, or you give the WAU a chance at creating something new. There is no way of knowing what choice is correct - because you don't know what the WAU is thinking. You never get to. You don't know its plans, you don't know if it even has the capacity to actually learn from its mistakes, hell, you don't even know if its capable of thought - but here it is. Making things. Terrible things, but there's a chance that it'll only get better with time. Simon himself is evidence of that chance. It has already managed to make what could be classified as a "complete" person. And if you kill it, Simon's going to be the last "complete" person it managed to bring back.
