Give John a Second Chance
Batman The Enemy Within Episode 4 Choices and Outcomes
After Bruce witnesses the horrific sight at the carnival, John also reveals that he’s figured out that Bruce is Batman as well. He starts acting more and more maniacal, and a lot like the Joker that we know. After a brief confrontation, he asks Bruce to give him a second chance. He says that he’ll track down Harley for him, and contact him once he finds her.
If you choose not to trust John, he’ll show up at Gotham Bridge during the final showdown and complete his transformation into the Joker. He’ll rescue Harley, blow up the bridge, and the pair will escape together.
If you choose to trust John, Bruce will agree but says that they’ll need to have a very serious talk once everything is over. The pair leaves the carnival together to go stop Harley. At Gotham Bridge, Bruce will try to reason with Harley before John takes over. He eventually manages to dupe Harley into handing over the virus, and the Agency is able to take him into custody.
However, Waller turns on John and tries to arrest him. John goes berserk and throws a smoke grenade to distract everyone. As Bruce tries to locate John, you’ll have a choice of either stopping an Agent from shooting John, or stopping John from stabbing Waller. The stab wound isn’t fatal, and John will make his escape. Before jumping off the bridge, he proclaims that he and Batman will bring justice to Gotham.