Dr. Buckley, was once a psychiatrist who specialized as an expert witness for criminal defendants. His testimonies would give the defense probable cause to have their clients released and put back onto the streets but now Buckley will face Nicodemus' judgment. Nicodemus retells the tragedy of Bruce Wayne and explains how Gotham's unrelenting nature gave birth to Batman. Nicodemus explains that Bruce tried to love Gotham for what it was even though its criminal element took away his parents but Gotham kept letting Bruce down when more and more people suffered the same way he did.
It was at this point that Bruce saw Gotham as a city of evil whose nature was to snuff out innocence where ever it may roam. It was then that Bruce knew why his parents were murdered, the city was giving him purpose as well as a mission to save the city from itself. In a way, Nicodemus implies that he knows who Batman is and explains to Buckley that the pain he is experiencing is not brought on by the city but by himself which gives his life very little purpose. Nicodemus ends Buckley's suffering by placing his hand on Buckley's shoulder. Within an instant, Buckley is set ablaze and burnt alive.
Commissioner Akins presents Batman with the string of murders that have been taking place in Gotham. Nicodemus' first two victims were Blaylock and Simon, two cops who retired ten years ago because they were under investigation by Internal Affairs. The third victim was Dr. Kelso, who worked for the mob as a freelance torturer. Buckley is the latest victim of Nicodemus but now two councilmen from City Hall have been taken. One of the politicians is fixture councilman Jack C. McKenna who has been involved in Gotham's politics for the last twenty years. The other councilman is Thomas J. Hart who was just newly elected to City Hall.
Akins says a witness saw Nicodemus getting into a getaway car after Buckley was murdered. The witness relayed the license plate number to Akins and Akins tracked the license to a small time hood/ wheel man named Bill "The Stump" Delaney. However, Stump had no home address which left Akins with little option but to rely on the Batman Batman used his own database and found one of Stump's old haunts. He interrogated some of Stump's old drinking buddies until one of them gave up his location.
Stump was ordered to meet Nicodemus at the Tri-Corner Yards where he was holding McKenna. Batman drags Stump from his getaway car and demands to know where Nicodemus is. Stump points to a nearby warehouse in the yards and Batman goes to intercede. Batman comes crashing into the warehouse, finds McKenna unconscious and smells accelerants. Nicodemus appears from the shadows and warns Batman to leave before he burns down with the rest of the warehouse. Batman calls on Nicodemus' bluff because he can smell the accelerants on Nicodemus' body and he wouldn't risk burning himself. Nicodemus smiles and says "I'm not too concerned about that." With the flick of his fingers, Nicodemus sets the warehouse on fire.
Batman grabs McKenna and heads for a window to escape while Nicodemus escapes. Batman lays McKenna on the ground and makes an attempt to enter the warehouse again in case Councilman Hart was inside. Batman hears screams for help coming from a room on the other side of the warehouse. Batman busts the door down and finds Councilman Hart chained to a furnace. Batman sets Hart free and helps him escape the burning warehouse. When they reach the outside, Batman reexamines McKenna and discovers that McKenna wasn't unconscious, he was dead.
At Gordon's precinct, the medical examiner discovers that McKenna had suffered a heart attack. It turns out McKenna had a medical history of heart related conditions. McKenna had gone through four open heart surgeries in the last three years. His last operation was about eight weeks before the kidnapping. Nicodemus figured by keeping McKenna away from his heart medication that McKenna would suffer a heart attack from all the pain that he inflicted on the councilman. Batman leaves the precinct and notices a chilling threat from Nicodemus on the jumbo tron in the middle of Gotham Square. Nicodemus warns the people of Gotham to leave the city before he burns it all to the ground with the aid of Mayor Dickerson.
Batman receives word from Alfred that there is a runaway train heading toward City Hall and Mayor Dickerson is tied to the front car. Batmobile races to catch up with the runaway train. Bruce uses his ejector seat to propel himself to the front car. Bruce notices the entire front car is strapped with TNT. Fortunately, Bruce cuts the hydraulics to the front car before it could make its intended collision. The next day, all of Gotham is praising Thomas Hart as a hero because he makes a public message to Nicodemus that the city of Gotham will not falter and it will not give into fear.
Gothams News makes an inspiring tribute to Councilman Hart's beginnings in Gotham and his efforts to the city as a man of the people. Hart was brought by Franklin and Eleanor Hart in Gotham's welfare system but he did manage to win a full scholarship to Gotham State University's School of Law. During his time in college, Hart became the president of his senior class and when he became a part of City Hall, Hart got involved with the city's welfare system. Batman found Hart's stardom to be a bit suspicious so he decided to take a closer look in the city's municipal records.
Batman checks into the child welfare care records and finds a connection between the Nicodemus murders and Thomas Hart. Bruce receives another call from Alfred that Nicodemus has struck again at the mayor's banquet. Witnesses say Councilman Hart was burned alive by Nicodemus who appeared out of the shadows when lights in the banquet went out. Nicodemus was able to sneak in because he rigged a circuit breaker with a timer switch. Nicodemus also used the flower arrangements at the banquet as a distraction for his escape because he had them soaked with a flammable but odorless liquid.
Batman and Akins take a closer look at the corpse that is supposedly Hart. The tuxedo on the corpse looks like Hart but Batman examines other identical traits and discovers that the corpse isn't Hart. The charred body is actually Benjamin Lutes who was sitting right next to Hart during the banquet. Batman discloses with Akins on how all the murders fit with Thomas Hart. First, the two crooked cops Blaylock and Simon were the investigating officers who were assigned to the Harts' murder case. However, the cops were paid to sweep the case under the rug rather than solve it.
It turns out Franklin Hart was one of the city's accountants and he was going to testify to a grand jury about a series of payoffs that Jack McKenna was receiving. McKenna hired Dr. Kelso to dispose of Franklin and Eleanor Hart while the two crooked cops kept everyone guessing on who could have murdered Thomas' parents. Dr. Buckley was paid by McKenna to keep Thomas under close observation because Thomas had become increasingly disturbed after the death of his parents. When all is said and done, Batman and Akins make their way to Hart's home where they find a note in his cellar. The walls of the cellar were covered with newspapers about the Batman and his exploits as Gotham's Dark Knight. Hart's note is for the Batman. Hart expresses his respect towards Batman's efforts to clean up Gotham but he finds Batman's non lethal approach on crime to be inadequate. Hart tells Batman that he will one day return to cleanse Gotham in fire.