It's clearly stated in-game that the reason the WAU killed everyone in Omicron was because Omicron was a direct threat, and various staff members at Omicron had a plan to destroy it via modified structure gel. In the WAUs view, saving humanity is it's primary goal (in ANY form, including as mostly lifeless zombies), but in order to achieve that goal, it needed to also survive. Thus, the survivors at Omicron had to go. By it's computational logic, the needs of the many always override the needs of the few.
That is
never "clearly stated in-game."
You encounter Ross, a deranged cyberzombie trying to kill the WAU for creating and torturing cyberzombies. He says:
"She was going to take care of it – But the WAU shrieked! They all died – But you, you! You took the gel from the cabinet".
Ross has every reason to say the WAU is deliberately attempting to kill humans, that it is trying to kill Simon in order to motivate him. Instead, he just says it "shrieked" without any further elaboration. He doesn't ascribe any desire or motive to it, despite having every reason to lie about how it works or genuinely believe so. He never says the WAU is evil because it is deliberately trying to kill humans and poses an existential threat to any survivors (such as those at
the other Carthage facilities across the globe). He says quite specifically that it is torturing the memory of humanity and that's why it must be destroyed.
Undelivered Report #3 – ‘Things are out of hand. The staff looks like they are about to explode. Every other person walks around with nosebleeds, and the rest keep wiping stains of blood from their eyes to keep them from overflowing. It’s to do with the WAU trying to free Ross somehow, for sure. At this point I wouldn’t be surprised if the body just got up and left. Raleigh Herber, our Dispatcher, has been snooping around asking questions she shouldn’t. She says she’s going down the abyss to find Alpha. I can’t bring myself to stop her….aaaaAAARRRGH!’
WAU was already messing with the blackboxes for days before the explosion happened. It's entirely reasonable to conclude that the explosion was an accident. No other time in the game or the logs does the WAU engage in radio warfare. Indeed Simon and Catherine never discuss this event, when you would expect them to be very disturbed by it (Catherine especially since they were her co-workers) or to worry that WAU might attack them to. Catherine herself is a skilled programmer who made immense strides in the field of brain emulation in post-apocalyptic conditions, and she has nothing to say about the WAU's behavior? What?
Also, undelivered report #3 had an unvoiced subtitle removed in patches:
"No need for the company to be worried, if she does go into the abyss, she won't make it far, she .... argh!"
The "company" here meaning Carthage; remember,
they have other facilities. The fact that her head explodes right after she says this is obviously meant to imply that Carthage is responsible, murdering Raleigh to prevent her from interfering (and killing everyone else in the process, maybe not intentionally). This line was removed in patches, which suggests it was part of a (sub?)plot removed during development in which Carthage played a larger role and was likely antagonistic.
Perhaps the most damning bit is that the WAU makes no attempt to stop Simon from using the reset gel. When he walks right up to it, it lets him plug into it through a convenient plug and reset it to factory default. Why would it blowup Omicron but create a plug to let Simon kill it? The murderbots obviously don't discriminate, since they attack Simon (and presumably each other). The WAU does nothing to stop them from killing each other and human survivors? Why?
For that matter, how could the WAU simultaneously be smart enough to adopt a utilitarian philosophy but be so stupid as to think insane murderbots should replace humans? If it's smart enough to understand utilitarianism, then it should be smart enough to avoid the many problems it causes. If it can create the talking "Frontflesh" in the
Transmissions videos based on photographs and voice logs of a personnel's family, then it should be able to hold a basic conversation like a modern LLM given that
it is a century more advanced than current LLMs. But there are numerous inconsistencies in the WAU's various experiments that suggest it doesn't really learn from trial and error, or at least not very well. It somehow managed to make wildlife populations rebound after crashing according to one terminal, but all its other experiments are horrific cyberzombies, fusions of humans and sea life, humans minds stuck in robot bodies that quickly go insane, and whatever the hell the Frontflesh is. There's no rhyme or reason to any of it.
Being able to think in utilitarian terms and plot mass murder for the sake of a hypothetical future necessarily requires the WAU to be an AGI (i.e. human-level or higher intellect), but there's no other evidence anywhere that's the case. Quite the opposite, the WAU seems vastly less advanced than current algorithms despite having vastly more responsibilities than we give to whole teams of humans and able to create things like the Frontflesh. You really find it believable that WAU can simultaneously think in utilitarian logic and plot mass murder for the sake of a hypothetical distant future, while simultaneously it is stupid enough to think insane murderbots killing each other are a desirable goal and is too stupid to communicate even by facsimile like our current stochastic parrots can?
I don't believe the WAU deliberately slaughtered Omicron because that requires way too much competence and forethought for an AI that otherwise behaves like it doesn't understand the consequences of its actions. I believe claims that it deliberately slaughtered Omicron according to utilitarian logic are pure projection on the part of commentators.
EDIT: I saw a convincing
hypothesis on reddit speculating that the WAU was trying to
communicate with Omicron and killed them accidentally when it was trying to explain itself but they didn't understand.
EDIT: I just remembered that one log mentions the blackboxes are installed with "Failsafe CRTH4", another part of the Carthage conspiracy I mentioned. It's mentioned in
this timeline.