He catches Markus and rest of the crew stealing stuff and is about to report them to his superiors. A human guard named Mike will be walking over and calling his name, during which Markus can either kill the guard, hide or grab John and hide. If grabbed and pulled into hiding with Markus, the player has the choice to release him to the human security guard, attack the human security guard or hold him until the human guard leaves.
If you kill the guard he will not say anything and if you hide without grabbing him, he will tell the human guard that there are deviant androids present.
After hiding with him he will not alert the guard and lets you steal freely. Once you begin releasing some AP700 Androids, he will ask you if he can come with you to Jericho. If refused, he will be angry and call you no better than humans and set off the alarm. If you accept, he will thank you and tell you how to get more parts if wanted. If able to steal the extra biocomponents successfully, he will be seen in Jericho.
If Markus gets caught by security in the security office, Markus and others will run away, including John. John will get attacked by a security dog. Markus can choose to leave or save him but will die anyway.
If John followed Markus and is part of the peaceful protest route and decides to sacrifice themselves while standing their ground, John comes to defend Markus before he can be killed. Markus will have a flashback of John when they first met. While the other androids flee in terror, John sacrifices himself and is killed by the riot police as Markus and the others escape to safety. He will look at Markus until he is destroyed by the police
In another choice, if Markus decides to charge at the police. John will be seen fighting a riot police officer and it is unknown whether if he survives the fight.