Omnitron rebuilt itself, in a humanoid form, and approximated an empathy-component. However, this proved to be its undoing! This new, tenth form of Omnitron realized with horror, a new emotion, that its previous purpose had been death and destruction! It focused its new efforts on returning to its point of origin to destroy itself before millions of lives could be threatened!
I missed this originally. Somehow I'd gotten it in my head that Omnitron-X was a component of Omnitron's that had broken away from the rest of the collective and rebelled, not that Omnitron-X was in fact all of Omnitron, just with a shiny new emotion chip. That makes it a little creepier (which is good). The heroes aren't just fighting alongside the "good" part of Omnitron against the "bad" parts. They're actually fighting alongside the villain itself.