An even Darker SOMA [ending spoilers]

[MrSteve]

Couple things here.

The WAU is a self evolving A.I. It may not be conscious by our standards, but over time a form of consciousness could have developed, as a result of it changing it's running to continue it's purpose.

Human intelligence was formed as an evolutionary response to our environment, so it's safe to assume that an A.I with the ability to self improve could eventually come to some form of this.

Second: Why all the talk about WAU trying to get on board, or control the ARK?

The WAU's primary function is to preserve humanity. I don't think WAU interfered with the ARK project, because it also is a way of preserving humanity. Why would it need to stop/control something that fits within it's purpose? That's probably why it left it alone.

On a final note. We could see that WAU was getting better at keeping humans, human. It could be that it began to understand a little more about what 'preserving humanity' meant.