When the time came for the Spartan augmentations, he became crippled during the surgeries and could not continue his military career as a Spartan-II soldier. Despite his now defective body, Chief Petty Officer Mendez noted that Kirk and the others who can no longer fight still have sharp minds, and they were reassigned to a non-combat position within the Navy, specifically planning missions, analyzing data, and troubleshooting ops.
John-117 last saw Kirk in a neutral-buoyancy gel tank, breathing through a respirator alongside René-081, whose skeletal system, due to the carbide ceramic bone ossification, was also disfigured beyond recognition like Kirk's. Kirk and the other injured Spartans were taken out of the launch chamber of the UNSC Atlas by a few crewmen shortly after their surgical enhancements were completed. Kirk and the others' whereabouts and positions are currently unknown, though it is likely that he was permanently reassigned to ONI as Chief Mendez had told John. It is quite possible that Kirk has to stay in the neutral-buoyancy gel tank for the rest of his life, perhaps crippling any serious attempts at strategical planning.