What happens after the ending (Ross's concerns re: Simon and WAU)? (spoilers)

[THX1138]

Why did Ross want to terminate Simon? Is Simon3 destined to become the continuation of WAU?

[Abion47]

It depends on which choice you made in Alpha, obviously. If you decide to spare the WAU, then Ross wants to basically force-feed you to it in order to get the poison going. If you decide to kill the WAU, however, it get's a little less clear. What Ross says is that he needs to kill "the only one immune to the new pattern", and the reasoning behind this I think takes a little bit of digging and speculation.

So what the "poison" is that Ross is so obsessed over is actually the same sort of structure gel that the WAU uses all over Pathos II. The difference is that the WAU had filled the structure gel with a ton of instructions, basically embedding its will into the gel on a near molecular level, whereas the uncalibrated stuff had all of these instructions taken out. Now, the WAU is responsible for the structure gel, and it creates more all the time as needed. When it does this, it uses a universal blueprint as a basis for the new gel, so it is ready for use as soon as it is made. When the blueprint is overridden by the uncalibrated gel, though, it essentially forces the WAU to start a process that replaces all the structure gel in Pathos II with the uncalibrated gel - gel that, because it lacks the embedded instructions, the WAU cannot use. So while it doesn't strictly "kill" the WAU, it does neuter it, rendering it unable to do anything at all. This is what Ross was referring to when he was saying "poison the imprint".

As for why Simon needed to die as well, my thinking is that Ross reasoned that, in order to be effective, the uncalibrated gel needed to be entirely uncontrollable. Simon-3's body, however, is made of the stuff, so he's been controlling it the entire time. This would allow the WAU a way to save itself if the WAU ever got ahold of Simon-3, so Ross needed to make sure that would never happen.

Like I said, though, that's just my theories based on what I could find on the subject as well as a certain level of speculation on my part.