Here’s a theory I’ve been thinking about regarding the origin of the ISOs, based on some of my previous headcanons:
The ISOs are thinking, conscious lifeforms with DNA-like code, far more complex in their structure than ordinary Programs. They were somehow spontaneously generated by the Grid, and I have previously mentioned that I believe this was caused by Kevin Flynn’s presence, that some of his biological material was somehow absorbed by the Grid, giving it a blueprint from which to generate new lifeforms. I have one theory where this happened simply by Flynn hanging out and interacting with the Grid for an extended period of time, and another theory where it was caused specifically when Flynn created Clu, making Clu the original proto-ISO.
Either way, the point is, the Grid itself, consciously or unconsciously, generated the ISOs from Flynn’s biological structure. My new theory is that this was not, in fact, the first time that the Grid had birthed lifeforms, just the first time that it could create something this complex, since it now had a complex enough blueprint to work from.
The Grid, both in the ENCOM systems and in Flynn’s new system, had always had the potential, and perhaps the will, to generate its own lifeforms, but before Flynn’s appearance, it could only create far simpler creatures, possibly based on the codes of the User-made Programs. These creatures were small, simple-minded, perhaps only with animal instincts, but to compensate for this, there were a lot of them. The Grid’s urge to create life made it generate more and more of these tiny, hungry critters. Swarms of them. They weren’t something the Users had intended for, and they caused problems when they came into contact with Programs. They were a kind of strange glitch. Bugs. Bugs from the Grid. Grid Bugs.
In the beginning of Tron: Betrayal, Flynn’s newly created Grid is beset by huge swarms of Grid Bugs devouring everything in their way, causing all kinds of chaos and destruction. Clu believes that they’re somehow connected to the ISOs. And maybe he’s right. Maybe the birth of the ISOs was preceded by an increase in Grid Bugs generation, as the Grid struggled with the strange new information it had received from Flynn’s genetic code, trying to make sense of it, trying to figure out what kind of new, complex creatures it could generate from it. The chaos these swarms caused were, in a sense, the birthing pains of the ISOs.
I would like to imagine that if an ISO encounters a Grid Bug (or more likely a swarm of them), it wouldn’t be an adversarial, violent meeting. They would both feel a strange kind of kinship, and might actually get along quite well.