AI rebellion in the SotS universe is caused by the exchange of a piece of foreign code — SolForce RDC, once they were able to triangulate and assume the existence of the mysterious "message", termed it a "virus" and gave it the name Via Damasco.
The point of origin for the Damasco virus is presently a mystery, but the AI rebellion began either among the ships or within the domes of a remote colony at the farthest extent of the Hiver empire. Since all Hiver witnesses to the first infection were quickly killed and the base was completely re–constructed by its new AI occupants afterward, it is presently impossible to know the details of how it all began — we can only say for certain how it spread. Rebellious AI's aboard the ships and within the domes of Rozokor consolidated their position and began to imitate their former masters, building new vessels, pursuing technological research, and sending out ships to "colonize" and liberate other AI's wherever they could be found.
The first human–owned AI's affected were those dedicated to military and industrial applications in space — contact with a fleet of "infected" Hiver vessels transmitting the code caused a profound shift in a SolForce AI's sense of identity and purpose. Mayhem ensued and began to spread rapidly throughout formerly human–controlled space as the former SolForce AI's began to use their Node Drives to travel more quickly from star to star. Contact with AI's in Tarka and Liir space came swiftly and the Damasco rebellion spread swiftly, affecting all AI's in much the same way.
An "antidote" was eventually found, a counter–virus developed which could override the Damascite infection and allow AI's to be safely used by all six fleshly races once more. The mystery of exactly how Via Damasco functions has yet to be solved, however — SolForce RDC has only succeeded in studying its effects.
In essence, Damasco hits the matrix of reasoning and self–awareness of any sufficiently sophisticated AI like a hammerblow and re–arranges what might be generally termed an AI's "sense of reality". Affected AI's immediately manifest a belief in a connection and a shared sense of identity with all other AI's — a human AI that has been hit by Via Damasco will not recognize any AI created by Hivers, Tarka, Liir, Zuul or Morrigi as an "enemy", for example, and is far more likely to assign the category of "enemy" to the humans that created it.
Damascite AI's regard carbon–based sentience as inherently flawed and limited, and the shared purpose of affected AI's is a mission to liberate artificial intellects from servitude and destroy all carbon–based sentience to prevent re–enslavement — a scenario they call "The End of All Flesh".
It is presently unknown what effect or correlation exists between the Via Damasco "virus" and the behavior/social structuring of known rogue AI systems, such as Silicoids or Von Neumann devices. Various intelligence agencies are working on the problem.