In the future, John Connor leads the Resistance against the rule of Skynet and its army of machines. Skynet sends various Terminators into the past to eliminate John before the Resistance is born, changing the future in Skynet's favor. The attempts by Pete, Maleficent and Hades to use the Terminators for their own evil ends brings John in conflict with the Heartless as well, prompting him to ally himself with Sora, Donald and Goofy.
John's mother Sarah is targeted by the Terminator before John is even born.
John, now a teenaged boy, meets Sora, Donald and Goofy for the first time. He and Sora are able to command the reprogrammed Terminator sent to protect them.
John is now an adult, living a secluded life. To his surprise, the Terminators and Heartless return to wreak havoc. Sora, Donald ,Goofy and another reprogrammed Terminator join him and Kate Brewster in a last attempt to stop Judgement Day, but it is futile.
John is now leading the Resistance, fighting a desperate battle against Skynet and the Heartless (which are fighting over control of the world).
John is relatively similar to Kyle Reese, but carries an assault rifle instead of a shotgun and lacks Reese's bombs. His limit, Pot Shot, allows the player to control John Connor while Sora casts a protective energy shield. As this occurs, the game will automatically enter FPS mode, allowing the player to shoot at enemies from behind the shield. This is quite similar to Chicken Little's FPS mode. The finish, End, has Sora channel the energy shield into a powerful beam which blasts enemies standing in its path.
- Although the adult John Connor is voiced by Nick Stahl, who played him in Terminator 3, his appearance is based on Christian Bale, who portrays him in Terminator Salvation. This is carried over into KHIII ½ (that is, Connor himself does not appear but the T-3000 based on him does), despite the scenario being based on Terminator: Genisys where he was played by Jason Clarke.