Well, nothing says that nanites have to be "permanent", and some nanotech has transient uses.
I second the fact that nanotech is used in leonization and for bridging the connexions to neural system.
It was in shadowtech, and told again in man and machine and augmentations.
One guess is that simsense, in a broad sense, could be used.
Since simsense is stimulating the would neural system, it is the perfect way to
remodel neural connexions. Cause in the end, when taken in simsense, you never
know if it is real or not, so it should have the same effect than real experience
(at least, with all failsafe removed, like in BTL and personachips).
I guess that development of nanotech neural amplifiers was a step toward this.
Maybe there could be a relationship to something that came from above,
but maybe there are also sequels from the beginning of the new matrix.
After all, we never knew what became the AI and the Jormugand.
Since spontaneously AI appeared, then, it means that somehow the X
factor that made AI what they are disseminated, and I guess the Jormugand had a role to play
into this.
And then, there would be some signal or semi autonomous foreign tech.
And it would become sentient, by the grace of meeting this.
Since spontaneous AI are said to be related to their original programming,
maybe this foreign tech was meant to collect infos about us, as a spy, or an arbiter.
Or had to evaluate if our tech could handle digital minds to save from extinction.
And then, it ran south.
Other possibilities, more down to earth, are psychotropic IC embarking knowbots
becoming sentients, and insanely powerful by inheriting both large chunks of the most
powerful AI on earth code, and dissonant power, with the knowledge of Deus to level the thing
(after all, it included some kind of mental programmation of the nodes of its network, if I remember well).
What I am fearing about is all the possibilities it opens for unwired critters becoming something
more too. Like being reprogrammed to run havok or act like an army, with an hive mind.
And what about weaponized biodrones (largely developed using nanotech).
And that is not even considering unwired critters gone "shapeshifters", in matrix, what would it be like?
At last, that is just the tip of the iceberg. The wolf's killer was stupid enough to show off.
But what about the ones who would retain most memories of their victims, blending in the masses,
running their strange agenda, maybe without even being conscious of it in surface.
Hope the possibility does not exists and that somehow, they have to take the whole personality and
be acting in design. That would make them, even with memories and skills, a lot more obvious
and previsible opponents, that could be tracked by personality tests, "lie detectors" and mind probing.