It wasn't the software it was the nanites. Well it was the software but the addition of the nanites helped it go more rogue and self reliant. I have a theory or such about Control from Star Trek Discovery season 2. Yes it was software, et al software that had gone rogue but I think it was the addition of the nanites that made it a little more sentient then it originally was, that's my theory. Also where did they come from? Were they the same nanites that Jonathan Archer found in the Enterprise episode "Regeneration" and were taken from the Borg they found frozen on Earth? Also why the hell were they even carrying a stock of those on the ship? Why the hell would they even need a stockpile of active nanites? I know Section 31 but why would you carry things like that onboard your ship?