"The Black Mirror" is an overarching story crafted by writer Scott Snyder. The concept of the story is that Gotham City is its own character that reflects its seedy nature upon those who try and protect it. It focuses on two main protagonists, Dick Grayson as Gotham's Batman and Commissioner Jim Gordon. Gotham puts both of the city's protectors to the test, having Dick discover what it truly means to be Batman in Gotham as he sees a darker side of the city; meanwhile, Gordon's estranged son James Gordon Jr. returns to Gotham, bringing a dark past with him.
The story began in November 2010's issue of Detective Comics and wrapped up in August 2011. Originally, the title was planned to have Dick Grayson as Batman in the main feature (drawn by Jock) and Gordon in a backup role (also written by Snyder), drawn by Francesco Francavilla. When DC dropped backup features from all their books, it was decided that Dick and Gordon would alternate in the book's starring roles. Snyder would come to describe The Black Mirror as "one big story" with both Dick and Gordon's plot lines intersecting and interacting with each other numerous times.
Shortly after Bruce Wayne appointed Dick Grayson to be the Batman of Gotham City, a string of mysterious crimes occur involving weapons from the cast of Batman's rogues gallery. Grayson soon finds out that there is a secret auction called the Mirror House, led by a man called The Dealer who sells weapons and items used by many different villains to the highest bidder. Dick disguises himself as a guest and infiltrates the Mirror House where the Dealer auctions the Crowbar used in the vicious beating of Jason Todd at the hands of the Joker many years ago. Dick's cover is eventually blown and he is exposed to a gas that causes him to hallucinate while being attacked by the crazed members of the Mirror House. He manages to escape, and after recovering from the brutal attack, attempts to take down the Dealer who manages to escape. In the end, Dick recollects how he never expected that kind of viscousness from the Gotham citizen and he feels that the city is getting meaner and wilder.
Meanwhile, Commissioner Gordon has his own problems to deal with; his son, James Jr. has come back to Gotham. When Barbara hears about her brother coming back, she's none too happy, claiming that James Jr. is a dangerous person, claiming he hurt, and possibly killed someone named "Betsy." Gordon doesn't know what to believe, but is soon confronted by his son. James Jr. tells his father that he's alright now, he's come to terms with the fact that he's on medication, and wants to start a new life in Gotham by getting a job at Leslie Thompkin's clinic. In order for James to work at the clinic, he'll need a referral, and knowing that his father is close to the Waynes, he asks if he can get Dick Grayson to help him. Knowing that Dick possibly feels the same way about James as Barbara does, he remains conflicted. While Gordon tries to deal with his son's return, he opens up a cold case, trying to capture a child serial killer known only as the Peter Pan Killer. In his confrontation with the killer, it is revealed that the killer tried to abduct James in the past while the Gordons were on vacation, but was scared nearly to death by everything surrounding the boy. It was this very same vacation where Barbara's friend Betsy went missing, originally leading Gordon to think that James had something to do with it. Unable to get a confession before Batman's intervention, Gordon is left even more confused about who exactly his son is.
Sometime later, both Gordon and Dick investigate a bizarre crime in which a corpse of a orca whale was left in the lobby of a well known community bank in Gotham. Inside the corpse is the body of a young woman, who was eaten alive. Gordon points out to Dick that the banks owner, Sonia Branch, changed her name sometime back and is actually Sonia Zucco, the daughter of Anthony Zucco, the man who killed Dick's mother and father. By all accounts, Sonia is a good person, completely detached from her father, but someone has it out for her as the woman in the whale's stomach was her co-worker and best friend. Before Dick leaves, Gordon tells him about James, and asks Dick to meet with him. He also asks Dick to give him his honest opinion, if he thinks James Jr has changed, or if there's something still "sinister" about him. That night, Dick tries to investigate why anyone would be harassing Sonia in such a way, but Sonia gives him nothing to work with. Eventually though, through a listening device, Dick comes to find that she's being harassed by a new face in organized crime by the name of Bixby Rhodes aka Roadrunner.
Dick confronts arms smuggler, Roadrunner, but is unable to find a definite link between his operations and the murder and whale carcass in Sonia's bank. Later that night he meets with Gordon who has brought Sonia along with him. Sonia admits to Dick that she was scared of him, and that he'd see her just as the daughter of Tony Zucco, what many have pinned her as. She denounces her father and his legacy, and explains that many of Gotham's older crime families had come to her based on her name, looking to see if she could "invest" their money for them, aka clean it up. She would turn them down, and wouldn't have a problem. But the new faces in Gotham wouldn't take no for an answer. One of them was Roadrunner and the other, the criminal who murdered her friend, putting her body in the whale, is a pirate by the name of Tiger Shark. Dick apologizes for his misconceptions of Sonia, and promises to make it up to her, by bringing Tiger Shark down. Off the coast, he searches for Tiger Shark, but doesn't have to look for long, as Tiger Shark's submarine finds him first.
Captured by Tiger Shark, Dick is not impressed with the "King" of pirates, viewing him as just another criminal in a fancy suit. He manages to escape a perilous situation with Tiger Shark's whales, but Tiger Shark gets away in the process, blowing a whole in his yacht, sinking it to the depths of the ocean. Due to his extensive training and planning ahead of time, Dick is able to surface from the wreckage unharmed, and with enough time to make his important meeting with James Gordon Jr. Dick meets with James in down town Gotham, surprised to see how much he's grown, and thanks him for the work he has done at the Thompson clinic. The conversation goes pleasantly enough, James even mentions he ran into one of their old acquaintances, Ben Wolff, a boy who once teased James. He continues to say that Wolff could be none the nicer now, and it's "funny" how some people have to grow into the people they're meant to become. Dick takes these words to heart, realizes something, and excuses himself from James.
Later, as Batman, Dick meets again with Sonia Branch. He accuses her of erasing the security footage so he wouldn't know where to start with her friend's murder, that way, Sonia could use Batman and direct him to Roadrunner first, then Tiger Shark, both criminals giving her heat, only one guilty of the murder. The situation becomes tense when Dick claims that he could have caught Tiger Shark if he knew about him first, but Sonia fires back that maybe he just failed. Sonia excuses herself with a falsely pleasant "goodnight, Batman," wich leads to Dick making it a point to say "Goodnight Ms. Zucco" rather than "Ms. Branch." As Dick leaves, he remembers a circus performer from his past, and what he said about his act, jumping from 80 feet in the air to a three foot pool of water, being all about judgement. Dick remembers the time he saw the performer judge the jump incorrectly, snapping his neck, dying instantly. Dick subconsciously relates this to his misjudgment of Sonia Zucco, but elsewhere, James Jr. enters the house that belongs to Ben Wolff, the same Wolff who teased him as a child. He descends into the basement where a tied up, mutilated Ben Wolff, missing all his limbs, jaw, and one of his eye, still alive and in agony, pleads for his life. James picks up a saw and asks Wolff "Now, where were we?"
Sometime later, Jim Gordon visits Leslie to get her opinion on his son. Leslie raves about James Jr. saying he's been a great help, and has even volunteered for the infant nutrition program. Though Leslie approves of James, something doesn't sit well with Gordon, and he manages to swipe one of the experimental pills that James takes for his psychosis. Gordon visits Barbara, and asks her to analyze the pill. After some tests, Barbara find that the pill is formulated to actually stimulate the brain to create a psychosis in the one who takes it. The two are puzzled, as there is no way that James could actually spread the drug, and it wouldn't even affect adult minds, due to the dosage. Then it all clicks for Gordon, the nutrition program at Thompkins clinic. James would have access to mass quantities of infant formula, which could affect the young brains of children. With this realization, Gordon books it to James' apartment. All while this is happening, elsewhere at Arkham Asylum, during a routine physical examination, Joker manages to escape from confinement. Gordon reaches James' apartment, but doesn't find him there. After further examination, he finds a box containing the key that belonged to Barbara's childhood friend Bessy, and was last seen the day before she disappeared on their vacation. Amongst that key, there are hundreds of other similar keys. Dealing with the thoughts of his son being what he feared the most, Harvey Bullock shows up and informs the Commissioner that the Joker has escaped.
With a gut feeling that the Joker would once again go after his family Commissioner Gordon calls his ex wife and James Jr's mother, Barbara Kean-Gordon, who was in Gotham, to warn her. But it's too late, and as soon as he gets to her hotel room, he finds her curled up in the tub, infected with Joker toxin. With Barbara Sr. in intensive care, Dick goes after the Joker while Tim Drake and Barbara Gordon analyze the toxin and hotel security footage. Dick eventually finds Joker in the catacombs under Gotham. During their confrontation, calling Dick "Little Bird," Joker claims he was waiting for "his" Batman to come back, and wasn't the one who attacked Barbara Sr. With Joker repeating "it wasn't me" something clicks with Dick, at the same time in the medical ward, Barbara Sr. wakes up and tells Jim "It was him, Jim! It was him!" Then, in Kord Tower, just as Barbara sees the face of her adoptive mother's attacker, James Jr. sneaks up from behind her, and attacks his sister.
The hunt for Barbara is on, as James keeps her hidden in a platform under the bridge he fell off of when he was a child. He eventually contacts Dick, who he has deduced is Batman, and the truth comes out. James sees himself, a human unable to feel empathy and those like him to be superior, seeing Dick as the exact opposite of him. He returned to Gotham to challenge Dick, ultimately breaking him mentally. Dick tells James that they've already figured out his plan to tain the baby forumla, making children like him, but James informs him that he has no way of knowing if he had done it already or not. The climax of his twisted plan would be the murder of his sister and father, both of whom are great supports in Dick's life, and without them, James thought Dick would give up. Finished talking to Dick, James goes to finally Barbara, but she is able to surprise her brother, stabbing him in the eye. But the pain doesn't stop James, as he stalks his sister who has lost large amounts of blood, only able to crawl away. But before he is able to reach his sister, Dick shows up, finding James via a cellular tracker he implanted when he met with James days earlier. Tending to Barbara's wounds, Dick allows James to escape, knowing what waits for him on top of the bridge.
Thinking he's free, James hails his triumph, but is shot in the leg by his father. James pleads with his father to wait, but Jim only says "no" and shoots his son in the other leg. James tumbles off the edge of the bridge, but Jim catches him, promising his son that he's not letting go this time.
Sometime later, Jim meets with Dick, who is disassembling the crime lab that the GCPD didn't use. Jim thanks Dick for all his work, but Dick shrugs it off as not a big deal. Jim stops him and thanks him "on all fronts" indicating he may know more than he lets on. Dick tells him he's welcome, and continues on to report that his findings on the baby formula were inconclusive. The two speak for awhile about why they stay in Gotham, despite it's nightmare like qualities, but both of them determine that they are to stick to Gotham for the long haul.
Though, down in the streets below, a mother walks with her newborn in a baby carriage. The baby's eyes are wide with a eerie look, indicating that James Jr may have succeeded with his plan, but only time will tell.