Story: (Sorry, this is going to be long)
We begin with a chase scene. Batman is chasing down a highly acrobatic and highly-panicked cat burglar. He's introduced as a terrifying shadow, and we are given a fugitive's eye view of him as he repeatedly turns up in a flanking position on the thief. Since at this point he's just an inhuman force of nature, our attention and sympathy should be with the thief, who manages to very cleverly allude him right up until being cornered in an alley. Our thief, still frightened out of her mind, backs into a corner only for Batman to wearily and tiredly approach her to put her in Batcuffs. Now that he's up close, she actually acts surprised and quickly goes from looking like a scaredy-cat to an incredulous and gabby, and ever so slightly flirty, femme fatale. Batman, now very clearly human, underestimates her and winds up getting sucker-punched by her after she picks her way out of his handcuffs, staggering him just enough that she can escape minus her goods. He takes off after her, passing a sign for Haley's Cirque...
Midway through his pursuit, we hear a police channel voice come on over Batman's intercom. He continues his pursuit, obviously determined to catch her, until he hears "Shots fired! Officer down!" at which point he angrily leaves the chase to head for the crime in progress. He arrives at a hostage situation, where a small group of environmental extremists, led by a red headed woman, are attempting to force a fortune 500 CEO to confess to ignoring EPA regulations so that they can pass sentence on him for his "crimes against nature." Batman quickly and brutally takes out the majority of the group, only to be temporarily halted when the red head takes a TV crew hostage after distracting him with an explosive. Silhouetted against the flames, Bats stares impassively while the red head shouts that she's just following his example and taking the law into her own hands, but uses the timely distraction of a cop to hit her with a bata-rang.
An obviously irritated and tired Bats returns to the Batcave, slowly removing his armor to show just how badly beaten up he is and get us a chance to know him as a mortal human. Alfred arrives and activates the Batcomputer's TV monitors, which show both multiple crimes and tragedies that Bruce Wayne failed to stop and an interview by Vicky Vale with Professor Hugo Strange (our big bad). Here Strange and Vale discuss his theory that Batman is acting as a kind of monster maker, drawing various criminals and monsters to Gotham, citing the rise in costumed crimes by mentally unstable individuals, noting that the red head, Pamela Isely, prefers to go by her "real name" Poison Ivy and shows strong anti-social tendencies that he believes were exacerbated by Batman's fame. Alfred and Bruce discuss this idea as well, with neither agreeing with it but both admitting there are some relevant points being made.
Meanwhile, we enter Gotham Penitentiary, where “Poison Ivy” is seducing a guard so she can slam his head against the bars, take his keys, and try and make an escape, dismissing him as “stupid man.” Her escape is interrupted when she runs into Strange’s TIGER guards, who subdue her and bring her before Strange in the prison’s garden. Strange discusses a rare flower with her, highlighting its uniquely toxic properties and carnivorous capabilities. She corrects him on some of the facts he spouts, with him acknowledging her past career as a botanical scientist who had the unique ability to handle poisonous plants due to an unusual immunity to most toxins and poisons. Strange then reveals that he has been handling the plant with extreme care since it’s actually Ivy’s and he knows she’s been experimenting on it. She acknowledges she’s been trying to use the plant’s spores to make a very specific but powerful toxin that would only be activated upon the plant’s flowering. Strange briefly alludes to the power he believes the Batman has over individuals like Ivy and how he believes that his attempts to either replace him or destroy him will require certain weapons at his hand. He asks her how she’s been changing the plant’s chemistry and she reluctantly reveals how she’s been subjecting it to incrementally harder environments. Strange then has her forcibly injected with a chemical cocktail to enter her in a near death-state and follows it up with an injection of a combination of her plant and one of his formulas; he’s going to use her as an incubator for the toxin thanks to her immune system.
Two weeks later, Bruce, who is truly acting like an obsessive insomniac at this point, is pestered by Alfred that he has slept through the last whole week and how he's had little outside contact with anyone who wasn't a criminal and needs to get out more. Alfred convinces a prickly Bruce to go out to the Mayor's gala at Ice Berg Lounge and enjoy the Flying Grayson's performance as part of the touring acrobatic show Haley's Cirque. Bruce only agrees to go because the mayor will be discussing important topics with Prof. Strange and because it will give him more time to scope out the Lounge. Alfred insists he take a date, with Bruce sarcastically pointing to Vicky Vale in an attempt to avoid it.
Cut to Ice Berg Lounge, where Bruce is escorting Vicky Vale, who comments how persuasive his butler was. The gala features a few sequences where Bruce actually finds Vicky interesting and engaging and where he uses his reputation as a drunken playboy to insult the slimy owner of the Lounge, calling him Ozzy. The fuming Cobblepot is distracted by his own arm-candy, a Miss Selina Kyle, and any potential fracas is broken up after Vale leads Bruce away, warning him not to antagonize "the Penguin." At the mayor's table, Bruce continues to act drunk but manages to ask some very interrogative questions to Strange, who reveals he's planning a truly massive restructuring of the Gotham incarceration system, moving inmates from Arkham Asylum and Gotham Federal Penitentiary to a central location inside Gotham where he will use "revolutionary" new treatment techniques. Strange again expounds on his theory that Batman has a god like power to create these powerful criminals by his mere presence, expositing wonder at how the Bat could bring out his opposite number in the Clown, disconcerting Bruce for mysterious reasons.
As the night winds down, everyone enters the theatre section, where they all sit at the VIP section, with Bruce maneuvering to sit between Vale and Kyle to both play up his playboy image and investigate Selina's purse-Cobblepott has been having trouble finding things all night, and Bruce surreptitiously finds that Selina's been picking his pockets. While Haley's Cirque begins, Bruce continues to annoy Vale by playing drunk and has some fun flustering her with his charm and stealing back anything that Kyle picks from him. He's obviously having fun, and his attention is taken away only briefly to watch a truly impressive performance by young Richard Grayson, and when he goes back to playing "who's the better thief" with Kyle, he is initially distracted from the horrible deaths of the elder Graysons, but a quick glance by him shows that the cords of their trapeze have been cut. While the rest of the crowd leaves, he stays and stares down at the now orphaned Dick.
In the Limousine after dropping Vale off at the news station, Bruce voices his desire to return to the scene as Batman and solve the crime to help Dick, but is discouraged by Alfred, who suggests he simply ask Gordon for information on the crime and try and see to it the boy has a secure future. A brief scene shows Batman ninjaing into Gordon's office to demand the report and getting out. Bruce also reviews a taped recording of the performance, getting frustrated because he notices clues that would suggest the lines have been tampered with, though Alfred notices they are very subtle and could easily be misconstrued into something else and they only really show the truth in hindsight.
Bruce shows some grave concern after looking through the evidence, as both he and Gordon have picked out two very dangerous suspects for the sabotage: the Penguin, for reasons unknown but having full access to the stage and control over the hired theater personnel, and Tony Zucco, mob boss who was snubbed by the Cirque when he requested a private performance for his daughter's birthday and with a history of previous sabotage. Since neither is known for being particularly sloppy, young Grayson's very calm and observant recounting of the night's event is the biggest clues that the sabotage is deliberate, so Bruce decides to have Alfred enquire child services for the boy’s state, since there’s a real chance that a corrupt cop may try and make fast money by leaking how important the kid is.
Grayson has escaped the children’s home, and is crying on top of the police station, where he overhears Detective Bullock and Montoya discussing Zucco and Penguin. We see him racing across Gotham’s rooftops towards Zucco’s address (he used his iPhone) when he is overtaken by Batman right outside Zucco’s hideout. The kid isn’t scared of Bats, but ends up subdued anyway. Batman places a tracker and then takes the kid back to child services, only to find small time thugs in the process of attacking the place. Batman, obviously pissed, sticks Dick in the Batmobile and tells it to go to “Location #3,” and proceeds to decimate the hired thugs with even more fire than before. He’s so focused on beating one particular thug, that he doesn’t realize that the cops have arrived to arrest him until they ignore his opponents and he hears they have direct orders from the mayor to take him down.
Meanwhile, Location #3 turns out to be the medical clinic of Dr. Leslie Thompkins. She actually comes out to collect Dick himself and the Batmobile takes off for Batman himself. She has him sit down in her waiting room, where he soon finds himself scoping out several newspaper clippings from her past on the wall, and also finds the clientele of the place to be varied, especially when Selina Kyle enters supporting her young friend Holly. While sitting in the waiting room, Kyle recognizes Dick and asks him how he knows Dr. Thompkins. Thinking quickly, Dick says his parents knew her. Kyle seems pleased by this, saying Thompkins must have met them while working for Doctors Without Borders, and even mentions how she first met her after she set up shop in Gotham. Their discussion ends up including how the clinic’s biggest patron is Bruce Wayne, with Kyle even revealing that Thompkins knew his parents and comforted him the night they died, pointing out an article where Bruce actually explains that himself alongside a small picture of him the night of the murder.
Interspersed with this scene we witness Batman escaping a siege by Gotham’s SWAT teams while waiting for his car, with him hearing an argument in the chain of command between the commanding Bullock and a group of TIGER guards attached to the group, and finding the TIGER guards to be a bit tougher than normal, pulling out some of his heavier gadgets to deal with them. After one particularly tough tussle, he takes a blood sample to see why the guard is so powerful. His Batmobile shows up, and an angry, tired, and edgy Dark Knight enters it, picks up Dick, and takes him to the Batcave. He tells Dick to stay there and contacts Gordon to let him know that he’s securing the only real witness to the Graysons’ deaths.
Batman analyzes the tissue sample, and when pestered by Dick, reveals it’s a specially designed neurological drug that increases the body’s base strength and resistance to Bane at the cost of a degraded neural system. He also reviews Dick’s testimony from that night, even asking him to repeat everything he remembers in detail. Dick does so, highlighting a suspicious looking stage hand and earning Bruce’s appreciation for his intelligence and bravery. Batman tells him to stay put, as there is just enough time before daylight for him to make one final interview.
We next have a scene where Batman infiltrates Gotham FP and interrogates one of the crooks he was assaulting, an event we see is witnessed by Strange through a hidden camera. Meanwhile, Dick is shown using his skills to make it to the hidden passageway to Wayne Manor, discovering who Batman is and meeting Alfred. The crook being interrogated dies suddenly from what seems to be a stroke. Batman makes his way home leading to three events: Dick and he talk and he decides to train the 14 year old how to fight crime, Strange uses the security breach to have the city council approve his plans for a central prison center called Blackgate, and Strange also visits the semi-lucid Poison Ivy to extract more of her deadly pollen, revealing her plant and her are intermingled and she is in great pain.
The next scene is one part training montage for Robin, one part detective montage as Bruce continues to track down leads and suspects continue to die, a reveal that Zucco is in hiding, and a continually pained Poison Ivy, who is further experimented on by Strange’s assistant, a the construction of Blackgate, which resembles a prison less and more of a fortress.