The Lin Kuei clan has trained the most feared ninja assassins for over 800 years by kidnapping children as new recruits. Complete submission to the Grand Master was demanded, disobedience not tolerated. Two of its assassins are en route to a warehouse to take part in the Lin Kuei Grand Master's new technological initiative: Cyrax, against his will, convinced they are headed for death; and Sektor, believing the new initiative is the future of the clan. Inside the warehouse, doctors watch alongside the Grand Master and a pre-cybernetic eyed Kano as two henchmen approach Cyrax and Sektor. The assassins easily account for the henchmen, revealed to be digital projections of robots. Cyrax vents his frustration by removing one of the robot's heads and throwing it at a security camera. The Grand Master gives the command to begin Phase One.
Unit LK-4D4 (Cyrax) and Unit LK-9T9 (Sektor) are strapped down, electrical wires and grease protruding from dissections in their bodies. Developments in speed and outer casing advancements precede weaponization and emotional recalibration, a procedure to maintain the subjects' memories while severing emotional connections to them, preventing visceral responses in favor of cerebral ones. Cyrax continues to struggle, displaying anger and discomfort. By far the most advanced of the cybernetic models to date, the ninjas are outfitted with their robotic casings ready for Phase Two: a practical test against a previous model before the Grand Master can give the command to automate the rest of the Lin Kuei.
Project Hydro is initialized alongside Project Cyrax and Project Sektor as the doctors observe. During the fight, Hydro manages to overpower his more advanced counterparts. When working together, Cyrax and Sektor disengage Hydro. Cyrax, previously showing the most resistance to the cybernetic automation, is the one to initiate the fatality by mercilessly decapitating Hydro and the human within. Project Sektor & Project Cyrax are complete and the command is given to begin automating the entire clan.