Batman is still paralyzed from his encounter with the Joker, who finally revealed himself after a long year. Though he is now in the safety of the Batcave, he has to force himself to overcome his paralysis by sheer force of will. He releases himself from the straps holding him up with a shout which alerts Alfred and Julia Pennyworth to his recovery. Unfortunately, their news is bad. The Joker made good on his promise to poison the city center with a virus. Julia explains that it is an airborne pathogen which spreads effectively through laughter. Further bad news is that Alfred has been unsuccessful in synthesizing an antidote, commenting that this may be the Joker's masterpiece. Every one of the nearly one hundred antidotes Bruce has made over the years failed as well. There is some new element to this virus that they can't overpower.
Bruce suggests that if they find patient zero, who must have had some resistance to have passed it on at the Gotham Presbyterian Hospital. He may still be in the hospital, and if found, Bruce may be able to figure out an antibody for the virus. On his way there, he calls to Jim Gordon who warns that Batman won't be prepared for what's going on in the city center. The virus appears to twist the feelings of love that people have for one another into feelings of hatred - and given how people revere Batman - he'll be Gotham's most wanted. Batman is taken aback when he glides over the streets there, and sees crowds of infected coming to mob him. He steels himself, crashing through an upper window of the hospital as Jim explains that it is the oldest hospital in the city - and prone to tragedy.
After Batman signs off, Jim continues his research, noting that the hospital is also considered one of the most haunted place in Gotham, just behind Willowwood Children's Hospital. A fire was the first of the unexplained events that began those rumours, resulting in nearly fifty dead patients. As he looks through old newspaper clippings, the cigarette drops from his lips as he stares in horror, seeing the Joker's face in the background of a photo dating back to that fire from 1910. Moving forward, he looks at an article from 1946, when medicines were exchanged for poison. Again, the Joker appears in the background of the press photo. Incredulous, Jim sifts through his old photos of the day that both of his children had their tonsils out at the hospital, and is sure he sees the Joker in the background, peeking in on them. Hearing a creak from his closet, Jim grabs his gun, and approaches it, warning whoever is inside to come out. Suddenly, a boxing glove on a spring knocks him to the floor next to his bed, and from beneath it, he hears the Joker sinisterly offer a "knock knock."
In the hospital, Batman approaches the ward where patient zero is being kept. Before he can finish entering the code to get inside, he is surprised to discovers that patient zero is Joe Chill - the man who killed his parents. Suddenly, a set of stage-lights blinks on, and Batman is treated to a mock-up of Crime Alley on the other side of the glass. He sees Duke Thomas emerging from the rough-shod version of the Monarch Theatre, where he and his parents had once come from before they had their fateful encounter with Joe Chill. The Joker knows.
The Joker crawls out from under the bed and expresses his displeasure that Jim doesn't seem to want to listen to any of his new material - which is a shame, because he's got lots of it. He snaps his fingers, offering an example, and instantly, the curtains of Jim's bedroom ignite with flames.
Unable to stop it, Batman watches as Duke his parents are approached by Joe Chill with a gun, even though the man wishes to resist killing again.
Jim scrambles to his feet, pointing his gun at the Joker and warning him to drop the jokes and gags, and to stay put or he'll shoot. The Joker grabs an axe from the floor and offers that he will drop the act today. Today, this isn't a joke at all.
While Batman breaks through the glass and leaps into the path of the bullet fired by Joe Chill, stopping it against his Kevlar chest-plate, Jim fires his own weapon at the Joker, and hits him square in the chest, dropping him to the floor. Unfortunately for Batman, breaking through the glass allows the other infected to come through and mob them, infecting Duke's parents.
Batman hurries Duke away, Jim makes the call to Batman, tearfully expressing his relief at having actually killed the Joker. Batman listens, steeling himself against the infected newborns in the maternity ward. Jim's relief, however, unfounded, as the Joker rises to his feet behind him. Batman hears his scream and calls out, but it is not Jim who answers. The Joker greets him by addressing Batman with his real name.
