A young teen is running from a gang, chased into a subway where the lights suddenly explode. The leader of the group chasing the teen sees a silhouette, and demands to know who's there. The figure walks past the teenager who tripped, slowly stalking forwards, stepping into the light.
No reply comes, the leader growing angry and yelling as he charges at the dark figure, the rest of his gang moving behind him. The dark figure avoids each and every one of their strikes, while his counters are fast and hard. Soon, all are on the ground, the leader himself looking up at the figure in fear as it approaches. "W-What are you?!"
The figure lifts him to his face...
"I'm Batman."
...Then knocks him out.
Batman then turns to the fallen teenager, who is petrified at his approach. He closes his eyes... and opens them confused as he feels Batman comforting him, cleaning the dirt off his face reassuring him it's all going to be alright. Batman accepts a tearful hug as the teen admits to stealing cocaine from the gang's hideout, which Batman takes and then gives directions to the nearest Wayne's children shelter. The teen is terrified the gang will follow him, but Batman assures him they won't, a serious look in his eye convincing him to follow through.
Later on, in the gang compound where the drugs are being packaged and prepared to be taken out as the gang leader starts shouting instructions. Suddenly the lights go out, gangsters start panicking, taking out their guns, looking around as a cacophony of noise overtakes the leader's attempts to control the situation. Without anyone's notice, one by one, the gang members are taken down, brought into the darkness without anyone noticing. Until a single member finally notices and gives a shout before he's silenced.
"It's the Bat!"
All hell breaks loose as Batman comes out into the open, the fear he's infected them with causing half of them to flee outright, while the rest are taken down either by Batarang or fist. The leader tries to rally his men as he fires his gun, all to no avail, growing more and more fearful as his men are taken down, until finally he's the only one left…and no one's there. He fearfully points to all directions, at every sound, shooting everywhere until there's no more bullets left. He screams...
"Where are you!"
"Here" a whisper replies from behind, as he turns and gives a shout...which is cut short.
Police sirens are heard as the police gather near the gang's headquarters. Both James Gordon and Sarah Essen turn up to the scene, finding dozens of gangsters tied up and their warehouse on fire. Gordon hears the report as Sarah looks at the captured gang members, noticing some of them have been brutalized beyond what one would expect. As she moves to speak with Gordon, she finds him sneaking away to the back alleys after noticing a figure, where he meets with Batman as they discuss the crime in the city and its changing structure.
Despite the blow to the Falcone family, and the purge of many corrupt officers, crime has yet completely decrease; a new figure, calling himself the Penguin has risen up and brought a new wave of crime, taking over from where the Falcone's left off. Meanwhile, the Falcones have welcomed back in the Maroni family, an old Gothamite family that they'd once expelled, marrying Sofia Falcone to Salvatore Maroni. Their combined resources could prove a challenge for both the GCPD and Batman. Both assure each other however that they are making changes that will better Gotham. Though Gordon stated they have to become more focused, beating up vassal gangs is meaningless in the end, they need to seek proper Justice.
Later at Wayne Manor, during a GCPD fundraiser, Bruce Wayne is making the rounds, playing up his persona, as he meets Captain Gordon, his daughter Barbara and Sarah Essen there. Bruce and Gordon speak, with Bruce making himself look like a fool or ignorant about matters, even talking about the Batman like an "old wives' tale". While Gordon can't speak in favor of Batman, he still tries to remain neutral. Sarah is no that polite though, as she takes the opportunity to lambast the Batman for his lack of accountability, for being selfish, and in a moment of candor mentioning it's a fruitless crusade (as she's starting to get worn down by everything in the city). Both Gordon and Bruce are surprised but keep their masks on, as they continue this debate in a small way that allows Barbara to cut in, praising Batman for helping the city. Thus the debate turns to Barabara and Sarah, as Bruce skillfully moves away.
Later during the night, a man of well means is returning home with his wife and kid. They are well off family, the man receiving a call from his boss, revealing himself as a Lieutenant from the Falcone Family, now the Falcone-Maroni Alliance. The phone call keeps him busy, not revealing who it is and annoying him to the point the man threatens whoever is calling him. The voice on the other side asks him if he knows where his wife and children are now. The man realizes he hasn't heard a single voice since he picked up the phone. The call hangs, the man calls out to his family, but there's no answer. He runs through the house, opens door after door, and arrives at his child's room, where he sees his wife and children, all scared and unmoving, with a bomb in place counting down, a message near them that basically tells them the bomb will explode if they move, as well as a way to turn it off by solving a riddle.
We move to the outside, as the home explodes.
Later, perhaps by the next day, the GCPD is investigating with Gordon at the lead. Batman turns up at the murder scene where the cops are divided between those who support him, and those who don't, all from different reasons (there are corrupt officers, lawful officers, etc.) Gordon calms them down, but there's clear tension in the air. During the investigation Batman finds more and more clues that analyzing them has him find something everyone missed; a puzzle box. Solving it reveals the assumed name of the culprit, The Riddler, and within it its manifesto about the need to take back the city from the criminal scum running it.
Returning home Bruce starts working on what little clues there are, managing to find and narrow his list of suspects, but it's still a very long list. Alfred speaks to him about the case, with Bruce growing more frustrated at the lack of clues. Alfred brings up the fact that Sarah may be correct in what she said at the fundraiser, Bruce may be dragging others into his crusade, pointing out the Riddler may have been inspired to attack criminals by Batman, and others may choose the same path. Bruce however argues that what he does is to protect and promote justice.
"Justice, or vengeance sir? There's a clear line between both, and I fear for the day you may cross it."
Meanwhile Barbara Gordon is in her room, finishing with her martial arts training in her room (as much as she can in a small space, and with as little as she's been able to find). After her workout she once more goes back to her studies, her part time job as a librarian allowing her to take as many books in criminology and investigation as she wants. She hears her father calling for her and goes to greet him, hearing from him about his day at work and asking about the Batman. Though Gordon supports the Batman, he's concerned about him influencing Barbara too much, but she plays it off as being grateful for saving her. They speak about Sarah as well, how she's lately feeling more down, Barbara shows her concern, which Gordon appreciates.
She once more goes back to her room, taking a secret notebook that she hid from everyone, there she sees her notes on Batman, adding what her father told her, as well as a list of names of people who could be Batman; among the names there are Thomas Elliot, Harvey Dent, Matches Malone, Jack Napier, Bruce O'Brian...and Bruce Wayne. Before she closes it, there's a small drawing and design for a Bat suit...made to fit her. She then takes out another thing from her secret compartment, an old d police radio which she can use to hack onto police frequencies, listening to them, hoping to hear about the Batman's whereabouts.
After another night partying to protect his identity at another rich man's home, all the while Bruce wants to get out and go back to working on the case, he bumps into another of the Falcone-Moreni members. They talk for a bit as the help moves around them, and the man gives a message from Salvatore Moreni himself, wishing to speak with Bruce. He is confused, smelling a trap, but also willing to go and see if he can find something to aid him. Bruce receives a phone number and the man leaves to the parking lot, the Valet brings his car, he tips him and leaves. He soon finds an envelope in the other seat, which he opens and reads a message about his breaks being cut, and solving the riddle to find the other way out. Otherwise he will die. The Riddle proves too much for him, and he tries opening the door to jump out...which has the car blow up, killing him on the spot.
This time Batman is summoned through the Bat-Signal, meeting both Gordon and Essen, and shown the scenes of the crime, as well as the puzzle they found. This time it's closer toa Rubik's cube mixed with thematic images. Once more, Batman is able to solve it, and the information this time reveals pictures of Harvey Dent's assistant attorney, Gil Colson, cheating on his wife with a woman in a club they realize is a place owned by Sofia Falcone and Salvatore Maroni. Batman remembers the talk he had with Alfred, thinking that this person might be doing this in an attempt at copying him, and Sarah wastes no time in letting that known.
He once more moves, leaving Gordon and Sarah arguing the merits of the Batman, or even staying in Gotham and try to save it. No one notices Barabara Gordon, as she hides out of sight, listening to what they talked about.
Bruce looks at the pictures he found inside the riddle, his list of suspects growing lower as he's able to determine that whoever took this picture must have access to records from the police department from the quality of them. Thinking on the angle, the possibility of it being taken in a VIP lounge increase. Alfred mentions that even Bruce Wayne will need a reason for going into such a place, Bruce smiles as takes out the number he was given and sets an appointment. The next day Bruce arrives at the club early, when no one's looking he moves from his table and starts moving around, looking into the private and VIP lounges, looking at the different angles, finding the one place where the picture could be taken. He then sees Maroni arriving and he quickly makes for the table, arriving just as Maroni does, apologizing as he needed to use the bathroom.
He is welcomed warmly by Maroni, and during their talk many discoveries are made; Colson was on Carmine Falcone's payroll, and now works for the Maroni-Falcone alliance. Salvatore is his godfather, as he was Thomas best friend a long time ago. Even giving him the courage to ask out Martha in their youth. The reason he never managed to visit was due to the Falcones running him out of the city when Bruce was young. Now he has made an alliance with the Falcones via marriage, and wants to 'renew the relationship' between the Maroni's and Wayne's. Bruce is in shock, makes his excuses and flees.
At Wayne manor he gets in a confrontation with Alfred about what he heard from Maroni. Alfred at first does not want to reveal it, not when Bruce is clearly so in edge. He tries to calm him down, but Bruce is in no state to listen, leaving and sneaking into the GCPD as Batman, looking into files they may have relating to Maroni, verifying that just as it was said, Maroni had a connection to the Wayne's, but not one they could ever prove. There was even suspicion of a murdered journalist being traced to both Maroni and Thomas before the case was shut down. Bruce does not know what to believe, and is not willing to speak or listen to Alfred about it, throwing him out in a fit of rage.
Bruce goes to the funeral of the Maroni-Falcone lieutenant that was Riddler's first victim, looking to investigate more from those attending. He meets Salvatore and Sofia again, and also encounters The Penguin, who's presence causes discontent amongst his rival crime family, nonetheless Penguin attempts to point the blame for the Riddler at Batman, claiming the killer was clearly inspired by the vigilante, causing Bruce to worry about what Alfred said earlier. The Falcone-Maroni alliance to agree with Penguin, and swear to take down the Batman and Riddler.
The funeral is interrupted as a car crashes through the wall of the church, driven by Gil Colson, with a bomb strapped to his chest. Bruce is the only one daring enough to approach, attempting to solve the riddles locking the vest on to Colson as the other people flee. Bruce manages to solve the puzzle and save Colson, but also notes the lack of fear or panic on Penguins face.
Gordon and Sarah take Colson in for questioning, where he describes the manic behavior of the Riddler, disturbing Essen, who has to leave as Colson begins to describe the torture inflicted on him. Gordon and Essen have a conversation, where Essen reveals she doesn't believe the city can be saved, and that it's only getting worse, and asks Gordon if he would leave Gotham with her...
Gordon remains silent.
Meanwhile Batman drives down to confront the Penguin. Remembering the look of nonchalance he had at the church, as well as looking how the Riddler's actions seem to target mainly the Falcone's, leaving him with greater chances to gain more followers and businesses under his umbrella, he believes that he may be working with the Riddler, giving him information, or perhaps employing him. On his way he is ambushed by Maroni-Falcone thugs, and has to fight them off in a car chase before arriving at The Iceberg Lounge.
Hearing reports of the fight via the police frequencies she's hacked into, Barbara deduces where Batman is headed, donning some old clothes to hide her identity, she moves quickly, hoping to find and talk to him.
At the Iceberg Lounge Batman fights his way to Cobblepot, there he begins to threaten the Penguin, but despite his small size and being a cripple, Penguin refuses to break, getting more and more violent, Batman breaks his healthy leg, Barbara, having snuck in the back, hears this and flees, Batman chases her, not realizing who she is, she stumbles into a room with a dead body and a Riddler puzzle strapped to it, her scream making Batman realize who he was chasing.
Afterwards Gordon is enraged at Barbara for what she did and Batman for terrifying her. Cobblepot claims no knowledge of how the body got there, and as the Riddler has dumped his victims in odd places before, they can't draw a direct line to Penguin, letting him walk free. However Batman, contemplating his actions against the Penguin, thinking he inspired the Riddler, and seeing the scared Barbara, questions whether he is doing good, or inspiring people to hurt others or get hurt. Gordon talks to him, he does not know the answer to that, but he is sure that if it wasn't for Batman then Gotham would be worse. It's up to him whether he can continue down this path without losing himself.
Essen however is agitated and angry, leaving them and returning home. The next day Sarah is preparing to transfer to another city, asking James to go with her, but Gordon manages to convince her to wait, at least for a little while as with Barbara being traumatized, he can't think straight. When they get home Gordon finds and tears down Barbara's investigation journal, but does not find the Police radio.
Meanwhile at the Maroni-Falcone club Alfred goes in to confront Salvatore and Sofia, getting in an argument with them, trying to threaten them to stay away from Bruce, however a bomb planted by Riddler under the table goes off, injuring Alfred, while Maroni and Sofia escape.
Rushing to the hospital Bruce admits he feels Alfred was right, he has inspired people in the wrong way and was possibly fighting, not for Justice, but Vengeance. However Alfred reassures him he's fighting for the right reasons, but that he has to be aware what he does will cause harm to people, and cause people to enact harm on others, Batman is a force for good, but Justice comes with a price.
Alfred further reveals that, when Thomas Wayne and Salvatore Maroni were friends, Maroni's criminal background was a secret. The Wayne's and the police only found out when that journalist ended up dead. Thomas offered to turn witness against Maroni before he was killed. Alfred admits he doesn't believe Maroni killed Thomas, and tells Bruce not to pursue Maroni over vengeance, but for Justice.
Sofia Falcone and Salvatore Maroni argue over what's been going on with the Riddler. Sofia notes that it was lieutenants initially loyal to her who have been killed, and the bomb was on her side of the room, and accuses Maroni of trying to kill her and take over the Falcone's, instead of maintaining the partnership, Salvatore manages to calm her down, but then the camera pans to Batman listening from outside.
Sofia is arrested by Essen, who brings her down to the station. Sofia refuses to even talk to Essen, who leaves the interrogation room. From out of a dark corner steps the Batman. During his harsher interrogation he 'accidentally' lets slip the fact they're interrogating her due to Maroni. After he 'fails' to break her, Gordon comes in, and states that he is sorry for her treatment, but they had to make sure she wasn't in on it. He spins an elaborate, and fake story about The Riddler working for Maroni to kill threats to his power. Sofia, with her fears 'confirmed' agrees to have an intermediary (not herself of course) leak evidence of an old murder to the GCPD to get Salvatore arrested, the murder of the journalist all those years ago.
Gordon, Essen and Batman had worked in the elaborate trick together, the truth is they don't know who the Riddler is working for still, or even if he is working alone. Essen however is disturbed by Gordon allowing Batman so much leeway and access, Gordon again delays their fight by claiming they have to arrest Maroni now.
Batman, with the aid of the police, storms Maroni's bar and arrests him. However, as they do so he is shot via sniper rifle by Riddler. Batman gives chase, managing to avoid or survive several booby traps Riddler attempts to use to help his escape, capturing him and arresting him.
At the station Riddler is revealed to be Edward E. Nygma, the former corrupt coroner fired after Batman took down Carmine. Nygma reveals he blamed Batman, the GCPD and the Falcone's for the loss of his job, reputation and life. And so attempted to destroy the Falcone family via driving a rift between them and the Maroni that kept them in dominance, and in the process starting a gang war that would've drowned Gotham in blood and crime and ruined everything Gordon and Batman built.
Gordon questions why he's so open to admitting this, only for Nygma to state it doesn't matter. He's had a 'friend' install three bombs across the city, if he isn't released by midnight then the bombs go off and hundreds die. Further, Gordon and Batman HELPED him convince Sofia Falcone that the Maroni's were betraying her. With Salvatore dead, the two crime families will start a war anyway.
Batman manages to figure out via clues given by Nygma during his crime spree where the bombs are placed. He, Gordon and Essen rush to find and disarm the bombs, only to find each needs to be disarmed by solving a riddle. Gordon solves his by guessing, Batman quickly figured out the answer, Essen has no clue, Batman and Gordon try to rush to her location to save her, but it's clear they won't arrive in time.
Instead, through her radio, the voice of Barbara Gordon gives Essen the answer. It turns out she was listening in to the police frequencies again.
With the final bomb disarmed Riddler is judged and sentenced, Gordon publicly releases his statement early, making Sofia realize she was tricked, and continue her alliance with the Maroni's via her and Salvatore's child. She swears revenge on the Batman.
Essen meanwhile packs up and prepared to leave Gotham, she states that the city is becoming too much for her, that what Batman is turning it into, what he's making Gordon into, isn't something she wants to be a part of. Gordon replies he's never changed, he's always been someone willing to fight for justice, and he won't give up on Gotham. Essen looks at him, seeing his sincerity, kisses him, and replies that she cannot give her all to a city she does not think it's worth it. Then leaves, giving a final goodbye hug to Barbara, mentioning out of hearing that her research was on the money, now she only needs to trim it down.
Outside, before going to the cab, she enters an alley finding Batman there, knowing he would make sure nothing bad happened after the entire debacle. She tells him she respects what he's trying to do, but it's too much for her. Batman states there's a price for Justice, and he and Gordon are willing to pay it. Essen questions whether he's looking for Justice or vengeance...Bruce thinks back, on everything that's been revealed, and confidently states 'Justice'.
Batman meanwhile goes to the Martha Wayne Hospital and confronts Penguin, who now walks in a 'Penguin shuffle' with both legs due to Batman's beating and his original crippled leg. Batman states he knows Cobblepot was funding Nygma's revenge scheme, that he helped plant the bombs, that he was attempting to destabilize the remaining Falcone's so he could sweep in and become the cities great crime lord. Batman has no proof, but he will get it...eventually. Penguin is intimidated, but tries to puff himself up, looking away for a second, then turning to reply...but there's no one there anymore.
In the epilogue Bruce helps Alfred home after the hospital, promising to look after him. He hears a knock and opens the door to see Barbara Gordon, she looks at him, shows him her research notes. She knows he's Batman.
"We need to talk" she says, as Bruce invites her in, looking around to make sure no one followed her.
Meanwhile Cobblepot, Sofia Falcone, Sun Yee On, the leader of the Triad, and Cartel Leader Hernan Esposito all sit around a table, discussing the future, and vowing to end Batman once and for all.
