Operation Kronos required Syndrome to pit retired Supers against prototype units of his Omnidroid battle robot, under the pretense that it was a military project that had become rampant and needed to be shut down. Any Supers who failed to defeat the robot ended up getting killed by it or by Syndrome himself, and the data from the battle was recorded and analyzed.
When a Super succeeded in defeating an Omnidroid, Syndrome used the accumulated data to create an improved model. After using the new version of the robot to kill the Super who previously defeated it, the pattern started anew, with Syndrome gradually refining and enhancing the Omnidroid's design. This had also killed off many potential threats to his plans. His ultimate goal was to make it strong enough to defeat Mr. Incredible.
Eventually, Operation Kronos reached a stage where Mr. Incredible himself became the guinea pig for the latest version of the Omnidroid. The retired hero defeated the Omnidroid 08, but Syndrome used the data of the battle to build the Omnidroid v.X9, which successfully overcame his former childhood hero. Using the data from the v.X9's battle, the villain developed the Omnidroid v.10 and prepared to begin the final stage of his plan.
The new Omnidroid was deployed via rocket to attack the city of Metroville. Using a remote that controlled the machine's actions, Syndrome planned on "defeating" the robot after showing that the Supers could not, gaining glory for himself and eventually rising to fame as a "fake" Super. Unfortunately for him, the Omnidroid soon deduced the remote's purpose and blasted it from Syndrome's hands before turning on its creator. The Incredibles and Frozone had then went on to defeat the Omnidroid v.10, derailing Operation Kronos completely.
- Operation Kronos alludes to the Greek Titan of the same name, Kronos Lord of Time. He ate all of his children so as to forego a prophecy that foretold his downfall at the hands of one of his offspring until his youngest child Zeus, who was hidden by his mother and led a rebellion against Kronos, cut him into many pieces with his own Scythe, freed his siblings from Kronos' stomach and brought the prophecy to reality. Similarly, in the operation itself, Syndrome attempted to kill superheroes so he could pretend to be a superhero until his most hated nemesis, Mr. Incredible, killed him.
- It is also a reference to a science fiction film of the same name which features a robot that can only be destroyed by itself, much like the Omnidroids from The Incredibles.