What Happens to Harley and the Virus
Batman The Enemy Within: Episode 5 Choices and Outcomes
On the vigilante path, Harley and Bane are taken in by the Agency and used as Waller’s puppets to fight Batman and Joker. The virus will be a non-issue, as Joker hands it to Batman, who promptly destroys it. Harley and Bane show up at various points during the episode to try to thwart Batman’s plans, and it becomes clear that Harley herself has no more control over Joker.
On the villain path, Bane doesn’t appear in the episode at all. Harley and Joker team up as they plan virus bombs all over Gotham, and she shows up during the dinner party near the end of the game. However, Bruce and Selina team up to take down the villainous couple during the party, and Selina holds Harley down while Bruce chases after Joker.