Its highly likely that Control isnt quite as finished as we were led to believe, disabled yes, dormant yes but not dead and its still in the spore room as Discovery goes to the future.
Essentially the present is now safe but the future is still up for grabs, that is probably why we were not shown Burnham or Discovery at their destination.
According to Kurtzman Control is really dead. So what they said in the episode about Control being destroyed was a fact.
https://www.hollywoodreporter.com/l...y-season-2-finale-time-jump-explained-1203166
Speaking of Section 31, Control seems to be neutralized in the finale, but Discovery is technically taking it into the future with them. Is there a chance it could resurrect in season three?
All I can tell you is that Control is officially neutralized, but there will be much bigger problems when they get to the other side of that wormhole.
It is ridiculous how easy it was to destroy Control in the end. It shouldn't have just been in Leland. The program should have been in all Section 31 ships and should have been so smart to put itself into countless other places. As smart as it obviously was already, it should have already infiltrated the whole Federation network and numerous alien networks. Even current non intelligent computer viruses are seemingly better with distributing themsevles across the internet.
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