What happened to the UNSC?

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After Cortana and the Created uprising it can be presumed that in its first few days the UNSC was overpowered. Guardians would rise up from planet surfaces and emit an electro magnetic blast that would also obliterate the areas they rose from. Why some planets have these Guardians and others don't have never been explained but for the human colonies that faced the Guardians where the UNSC was present, the response was immediate and areas around the Guardians were typically restricted up until Cortana awoke all of them. 

Cortana wakes up these Guardians, broadcasts to the galaxy turning most smart AI's to her side and subsequently subduing the UNSC capabilities to fight because of the over reliance in AI. 

Its important to note that not all ships are capable to keep jumping from point to point to avoid Cortana like the UNSC Infinity.

So after a few ships fall from orbit from the EMP of Guardians (possibly detonating on impact) and that damage is done, it can be projected that Cortana through fear and organization with other military AI's set to change the hierarchy of the UNSC and use its mobile prowess to isolate military elements from pooling resources to fight back while also fulfilling a more humanitarian role, subjugating humanity in a way she best fits is probably in the vision of her experience against the covenant and protecting humanity (hence the destruction of the Brutes homeworld, especially when they did not cooperate) and while she did that later into her reign all other suggestive acts are benevolent. 

She really brought "peace" in that sense. The game failed to capitualate but this "Order 66" moment of Cortana founding the Created and turning all AI against humanity is a storyline that could and can still go so many ways filling the gap between game and books.