The movie starts with Batman sneaking into Arkham Asylum after hours. We see a shadowy figure of the Joker sitting on his cot. Batman comes to the door and addresses him. The Joker talks about how he is just biting his time before his next "performance" and is enjoying his time in Arkham insisting that he is making new friends and that he likes the lady doctor they've assigned him. He does however miss his "face". Upon being admitted into the Asylum, they took away his make up and he feels naked without it. He compares it to Batman losing his mask. Batman says that his costume is just used to fight crime but the Joker insists that it's his real persona and that whoever he is underneath is just a mere alter ego used to conform to the world around him. The Joker says we are born wearing mask and it's not until they alter their faces do they reveal who they truly are and cites Harvey 'Two Face' Dent as an example. He says that while wearing the "masks", we are more free to do what we want and that losing the mystery of what's behind the mask causes us to be tied down. Batman ignores the Joker and tells him that he will rot in the cell forever to which the Joker remarks that Batman will soon join him, knowing that his is Gotham's most wanted for killing Dent and five other people. The Joker then calls for the guards and tells them Batman is here and laughs as Batman flees.
Meanwhile, a drug deal is going down somewhere in a back alley of Gotham City. Guys with guns are meeting up to make an exchange. Just then, Batman lands crashes the party and starts beating up a few of the dealers. That's when the dealers reveal themselves to be undercover cops and suddenly, police search lights shine on Batman and SWAT teams have their guns pointed at him. The whole thing was a sting operation set up by Jim Gordon's replacement as head of the Major Crimes Unit, Harvey Bullock and Detective Ramirez's replacement Detective Nash. Batman manages to escape the ambush but gets caught up in an intense high speed pursuit with his batpod. He eventually loses the cops and makes his way to the newly rebuilt Wayne Manor/Batcave.
He discusses with Alfred how the cops keep getting closer to catching him and that it's making it difficult to do his job, especially with Lt. Bullock on his trail. Meanwhile, Detective Nash puts out an APB that an anonymous tip states that there will be a break in somewhere that night but it's in the form of a riddle and that all cops should be on the look out. Nash states the riddle over the radio and asks if any of the cops know what it means. Batman overhears the report through the radio and manages to decode what the tipster was trying to say and figures out that someone will be breaking into Wayne Enterprise. Batman stakes out the building while being on guard for Bullock and his task force. He meets up with Gordon on the adjacent building top to discuss the situation. They converse about how Bullock has tunnel vision for Batman and that even Gordon can't keep him under control and about how Gordon is sorry that this has to happen. Meanwhile, someone manages to break into Wayne Enterprise on the duo's watch and they don't know how. Batman swoops into action and lurks through the darkness of the building to find the intruder. He discover's someone is downloading something off a computer. He tries to stop them and is surprised to see it's a woman. She's covered from head-to-toe in a solid black suit with night-vision goggles and what appear to be cat ears on her head.
The intruder then attacks Batman as her files continue downloading. Batman is impressed with her karate abilities. She pulls out a small billyclub that shoots out a rope grappling hook and begins lashing at him with it. They continue to duel as Gordon is watching them and decides to call in for back-up. Eventually, her files are done downloading and she snatches her flash drive and flees. Meanwhile, the cops arrive just in time to find Batman who they believe to be the intruder. As he fends off the police and makes his escape, Catwoman watches and is impressed with his style. She reports back to a mysterious figure who asks if she got the files. She responds by saying : "Of course, but someone tipped off the Bat and the cops. You have a snitch in your little circle," to which the figure replies. "I wouldn't worry about it, after all you are the best there is, aren't you?...By the way, who came first, Batman or the cops?"
"Batman" she replied. "What do you want with those files anyway?"
"That's for me to know and you to find out," replied the figure. "I have another job for you..."
Lucious Fox discovers that the intruder copied files of all the entry logs of Wayne Enterprises for the past few months and that she is apparently a world famous thief that was named by newspapers as the Catwoman. There is nothing known about her except that she is very good at what she does and has never been caught. Bruce is at home depressed about the death of Rachel and the manhunt out for the Batman. Alfred convinces him to get out of the house and get back into the world to help uplift his spirits. Bruce reluctantly does so and goes to a gala event of some sort and meets Selena Kyle. Bruce tries to put on his billionaire-playboy act but she believes that's just for show to impress everyone and that there's more to him. They hit it off pretty well and Bruce has a good time.
The MCU receives a phone call with a distorted voice telling them to turn on the news. When they do, there is a video being played with question mark and a distorted voice stating he would like to play a cat-and-mouse game with the Batman. He says he will set up obstacles all over Gotham until he proves he is smart enough to catch him. He also states that even he does catch him, he bets him that he will get out of doing any jail time. The first obstacle is that there is a bomb planted somewhere in the city and Batman has 1 hour to locate it before it detonates. The voice leaves a riddle to the location. Bruce is watching the video and accepts the invitation. He asks Alfred if his "new ride" is ready and goes down into the Batcave and hops into a new sportier (but still armored and fairly bulky), solid black Batmobile. While exiting, the Batcave, Alfred reiterates the riddle to him as he tries to figure out what it means. Batman finally figures out what it means and discovers the location and calls Gordon to get the bombsquad ready. When Batman arrives on the scene, he discovers that the bomb has a video screen attached to it that informs him that there is a trick to disarming the bomb involving a brainteaser (riddles and brainteasers I will leave to the writers to figure out). Batman successfully stops the bomb just as members of the bombsquad and MCU arrive and attempt to aprehend Batman who makes an action packed getaway as Bullock was even closer to capturing him.
The next day, in the afternoon, Selina Kyle stops by Wayne Manor and invites Bruce (who has just woken up do to being out late the night before) out for lunch. The two spend the day together and get to know each other. Selina tells Bruce that just because every other billionaire acts like a pompous ass doesn't mean he has to either. She says how much good she sees in him and that there's better stuff he can do with his money other than buy hotels to change their "pool policies". At nightfall, they get very romantic but are interrupted by Selina's alarm on her watch. Both agree to part ways as they both claim they have business to attend to. That night, the cops get another anonymous tip that a break in will occur via a weird coded message and Batman intercepts the message yet again and manages to decode it. Batman discovers that the break in will occur at a bank and goes there as he waits for the intruder. He runs into Catwoman again who is not breaking into the vault but into the lock boxes. She is surprised to see Batman again but eager to face the challenge. The two spar yet again and just when it seems like Batman has her cornered, she trips the alarm and makes her escape. Batman, frustrate because he knows Bullock will be there soon, neglects Catwoman and makes his getaway. Catwoman, after getting a safe distance from the bank and the authorities, makes another phone call. She tells the person that she's calling that she ran into Batman again but the voice ignores that and asks if she got the book to which she replies: "Yeah I got it. There must've been a fortune in jewelry and family heirlooms in those boxes. Why did you only want the book?"
"The right information can be more valuable jewelry or material possessions, my dear." answered the voice.
"Yeah well, I hope you don't mind if I took some for myself."
"Not at all. I'll set up the time and place where you can collect your fee and then you disappear. Understand?"
After Bruce returns, he has a conversation with Alfred about getting a personal attachment to someone while he's Batman. Alfred tells him, he can't be afraid to let people but while leading a double life he is likely to lose those close to him through his secrets. The next day, there is another threat by what the news calls "this mysterious Riddler". This riddle is a two parter and Batman solves the first part which reveals that there is a runaway train full of passengers on the Gotham Monorail. Batman uses his batmobile to catch up with it and manages to get on while in motion using his grappling hook. He sees another video message saying there's a special way to stop the train. Batman manages to solve the riddle and the Riddler congratulates the Batman on his victory as the train begins to slow down but reminds him that he forgot about the second part of the original riddle. Just then, the last car of the train detaches and begins flailing on the monorail. Batman can't keep the car from falling and numerous passengers get severely injured while 6 die. Batman is angry while Bullock blames Batman for "interfering in police matters" and causing the deaths of 6 people.
Meanwhile, Batman is distraught and as Bruce Wayne, he decides to spend more time with Selina. They spend the night together and he wakes up the next morning to find her gone with a note that says "Went to work. Call later." The Riddler sends another message to the news and says that he has kidnapped "one of Gotham's finest" and shows a video of Detective Nash tied up with a bomb strapped to his chest. The Riddler says the Batman has one hour before he has another death on his hands. The Riddler gives him a riddle as to where to locate the detective. Batman, however is still worried that with all the hell raining on him that he will cause more harm then good so he passes the information on to Gordon and waits nearby as the cops raid the detective's location. They find Detective Nash strapped to the chair with the bomb, with Catwoman standing next to him. Though outgunned, the Catwoman makes a run for it however, Batman set up a trap just in case something happened and managed to catch her for the cops. The cops find her strung up by her feet and she is then unmasked and revealed to be Selina Kyle. Batman is shocked and grief stricken. They manage to disarm the bomb strapped to Nash before time's up.
Bullock interrogates Selina who claims she was set up. She said she has nothing to do with the Riddler and was supposed to meet up with her employee to collect her payment. They demand to know everything about her "employer" realizing that he and the Riddler are one in the same. She has nothing for them as the Riddler was very careful when doing business with her. Bruce hires a high priced lawyer to help her out, believing that she was set up by the Riddler for Nash's kidnapping.
During all this, Gordon receives a letter at his office with a riddle and deciphers it himself that says that warns that the Joker is about to cause some trouble. Gordon rushes over to Arkham to find the Joker lying in his cell. The Joker welcomes Gordon and asks why he's come to visit. Gordon has cops search his cell. That's when they find an armed bomb under his mattress. The Joker claims that he didn't put it there. Gordon orders that Arkham be evacuated and has the Joker placed under close watch.
Batman returns to where Nash was held to see if he can find any clues as to who the Riddler is and stumbles upon a tape with a question mark on it. It's the Riddler who says how disappointed he is that Batman didn't show up to the party and attributes it to Bullock's interfering with his game and states that once Bullock is gone, he will personally guarantee that the cops don't interfere with their game anymore and signs off without leaving any riddles. This puzzles Batman who immediately goes to track down Bullock to protect him. Batman plays the Riddler's tape back over and over looking for clues to in what he says to find out how he plans on killing Bullock. Immediately, Batman gets a hunch and calls Gordon to ask where the tips came from about Catwoman's burglaries. Gordon quickly asks around but can't find any kind of record as to where the tips came from. Bullock, in the mean time, is checking up on Nash to see how he is doing. Batman then asks who it was that sent out the original APB with the riddles. Gordon tells him it was Nash. Batman heads over to Nash's where Nash has already subdued Bullock and starts playing Russian Roulette but says he will pretend to be anyone or anything and gives him clues as to who/what he is (like in the beginning of Transporter 2 with the moon) and says everytime he gives hime a clue, he will spin the barrel of a revolver after adding a bullet and fire it at him. After a few guesses and clues given, Bullock has managed to get lucky buy always getting shot at with the empty chamber but Nash finallly has the revolver completely loaded and gives Bullock one final clue and says it's his last chance to guess what he is.
Bullock is facing his own mortality and admits that he cannot figure out the riddle and he says "Eddie, please don't do this," to which Nash mocks Bullock's stupidity and reveals that his name is actually Edward Nigma and that he is the Riddler. He tells Bullock that he shouldn't have interefered in his game with the Batman. Just before he pulls the trigger, Batman storms in and attacks Nash who fires off a shot, grazing Bullock, knocking him out. The Batman subdues the Riddler with ease but the Riddler laughs as he admires Batman's intelligence but says: "You may have caught me but as I told you, I won't spend a single minute in a prison cell...Mr. Wayne." Batman is shocked and the Riddler reveals he hired the Catwoman to steal information from Wayne Enterprise because he knew only that company would have produced the technology Batman uses in Gotham. He also said he had her steal records from the accountant, Coleman Reese, which helped prove that Bruce Wayne was Batman. He actually set up Catwoman to get killed during the police raid when he staged his own kidnapping. Also, his kidnapping was to put himself above suspicion of the Riddler so that when he killed Bullock, he would replace him as head of the MCU and keep the cops in the dark so he could continue his game with Batman. He says if he ever got caught, he was gonna use knowledge of Batman's true identity as a bargaining chip with the cops seeing as how he's wanted for the murder of 5 people (from the Dark Knight) and Harvey Dent despite the fact that he figured out Batman didn't actually do it. He tells him this because he believes Batman won't kill him as that's his "one rule" and laughs mockingly.
All Batman can do is hand him over to Gordon who arrests him and puts him in a police cruiser and gets in the back with him. The Riddler brags about how genius his plan is and mocks Gordon's relationship with the Batman as he knows there's nothing he can do to help him. Gordon disgustingly admits to how calculated his moves were but then says: "I still don't get one thing...what was the point of putting a bomb in the Joker's cell?" to which a confused Riddler replies "What are you talking about?" The driver of the police cruiser then says: "I think I can answer that." revealing himself to be the Joker. "See Gordon, I told you about my lady friend the doctor? Well she wanted to see me outside of work hours so she helped me concoct this little plan to get out using Mr. Nash here as a decoy."
"What are you doing here Joker?" Gordon asks.
"Well, once I heard that 'The Riddler' was gonna go blabbin' about the Batman, well I just couldn't let him spoil my fun." the Joker said. "All the fun is gone once we see who's really behind the mask. The Riddler here knows what I'm talking about. Look what happened to you once everyone found out who you were. Besides, people like jokes more than riddles anyway. HAHAHAHA."
Just then, the Joker draws a gun and tries to shoot the Riddler but Gordon struggles with him and causes him to crash. Gordon is knocked unconscious to find the car wrecked, the Joker gone, and the Riddler out cold but alive. Bruce talks with Alfred about Bullock still gunning for Batman, the Joker escaping, the Riddler slipping into a coma (thus keeping the Batman's identity a secret), and Catwoman in prison for all her acts of larceny. The film ends with Batman commenting on how he may need help in the future if he's to continue being Batman.