Batman: Arkham Asylum is the first animated film in the Batman: Arkham film trilogy and is set in the same universe as Rocksteady's Batman: Arkham video game franchise.
The film begins with Batman escorting the Joker in the Batmobile to Arkham Asylum after catching him at Gotham City Hall. The situation at City Hall took place at the exact same time as a 'mysterious fire' at Blackgate Prison, causing many of the prisoners to be sent to Arkham, among them a great number of Joker's own gang. When the two arrive at Arkham, Batman and several helmeted security guards strap the Joker to an upright stretcher and wheel him down into the Intensive Treatment Center. Batman accompanies the security personnel and the Joker to the Holding Cells, where the Arkham staff refuse to let Batman go any further. As the Joker is being registered into the Cell Block by Commissioner Gordon, he breaks free from a guard and escapes from Batman with the help of Harley Quinn. Batman, who is locked out of the area, breaks into the Holding Cells through a glass window. Once Batman is inside the Holding Cells area the Joker springs his first trap, unlocking the cells and allowing Blackgate convicts to flood out to attack Batman. After another brief confrontation with more convicts, the Joker deactivates a security gate, allowing Batman to follow after him despite Commissioner Gordon's observation that it was most likely a trap. Batman moves up a ramp in the direction of the Joker's escape, leaving the Holding Cells and entering the Processing Corridor, finding the hallway littered with fallen security guards the Joker left in his wake. He found one guard that had survived named Eddie Burlow, who points him to the Lower Corridor. Batman reaches the Patient Pacification Chamber, where two security guards inform him that escaped inmate Victor Zsasz has taken another guard, Mike, hostage and will kill him if he sees Batman get close to him. Batman subsequently subdues Zsasz after swooping down from a gargoyle. All of a sudden, Batman receives a message from Harley Quinn, who has taken Quincy Sharp, the warden, hostage. Although Quinn is convinced Batman is trapped in Patient Pacification, Batman escapes back to the Processing Corridor, moving into the Decontamination area, where several Arkham personnel and inmates were trapped in a room filling with Joker Toxin.
After clearing the room of toxins, Batman proceeds from the Decontamination area and follows several green arrows along the floor of the Transfer Loop that lead to the Secure Treatment Transfer room, where he is attacked by a mutated Blackgate prisoner. After a short battle the prisoner dies. The Joker escapes on top of a mobile security cell and broadcasts a message to Batman from a nearby guard station telling him that Frank Boles, a member of the security team assigned to escort Joker to his cell, is actually on his side and has captured Gordon. The Joker also warns that if Batman is caught following him, then Gordon will die.
Using a scanner in his cowl, Batman follows an alcoholic vapor trail left by Boles's bourbon through the Transfer Loop. As he nears the elevator to the upper level with security guard Henry Smith, Harley Quinn appears and blows up the elevator cable, hoping to trap Batman on the lower level, but he manages to scale the surrounding support structures. After a brief encounter with several pipe-wielding convicts, Batman approaches the Cell Block Transfer section, where he encounters the first goons carrying firearms, who have overwhelmed the security guards and taken control. He circumvents these armed henchmen and takes them down by stealth, before moving on to the entrance hall, where several armed convicts are patrolling the Intensive Treatment Lobby, armed with riot guns. After defeating them, he proceeds to the far side of the room and up the ladder to the raised hallway, at the end of which the Dark Knight finds Frank Boles dead, strapped to a stretcher near the exit of Intensive Treatment, having been double-crossed by the Joker, thus ending the trail Batman followed.
Simultaneously, the Riddler intercepts Batman's transmission system which he uses to contact Oracle, and begins tasking him with riddles which he can solve across the island. After solving the first of the Riddler's puzzles, Batman is approached by William North, an Arkham guard, who unlocks the door to the Utility Corridor for him.
Batman leaves Intensive Treatment, finding his way to Arkham East, where he discovers that the Batmobile is being attacked by Harley Quinn's henchmen. Fearing Gordon might be hurt, Batman instructs Oracle to deactivate the automatic defenses and decides to head for the northern part of the island, where it is parked. In the heavily guarded Arkham East Batman finds that many of the asylum's security guards had been lured to the area by a blind. Batman moves to a small connecting tunnel in between Arkham East and North. As Batman enters the smaller area he discovers a wrecked ambulance and a security guard taking cover behind it. The guard informs Batman of the armed Blackgate Convicts on the other side and Batman defeats the thugs, after which he rushes to where the Batmobile is parked and Harley Quinn's thugs are thrashing it. He quickly defeats the henchmen and follows a trail of pipe tobacco, left for him by Gordon, to the western section of the island, where Joker's men have also managed to take control.
After defeating two of the Joker's men attempting to make renovations to the Visitor Center to better suit the villain's taste, Batman finds a nervous guard attempting to hide in a watchtower, who informs him that the escaped convicts have seized the Medical Facility as well.
Entering the Medical Facility, he encounters Harley and Gordon but cannot reach them due to one of the security fields, forcing him to find a different point of entry through the Maintenance Access on the roof. He then uses the ventilation system to gain access to the Sanatorium. Batman then defeats five gun-wielding Blackgate prisoners who are holding Dr. Sarah Cassidy and three other doctors hostage. On his way through the facility Batman rescues several more doctors and staff, including Dr. Penelope Young, in whom the Joker's henchmen showed a particular interest. In the Patient Observation area Batman encounters security guard Aaron Cash and Doctor Kellerman, who are trapped by a trio of Blackgate convicts in a control room filling with toxic gas. After filtering the gas out of the room via ventilation fans, Batman heads to the Surgery Area, where he rescues Doctor Chen from a large number of the Joker's thugs. He proceeds back to the Sanatorium, pausing only briefly to halt a violent inmate armed with knives. Back at the Sanatorium Dr. Young insists on securing her research notes and is escorted back to the Arkham Mansion by Cash while Batman follows Gordon's abductors down to the Morgue level in an elevator.
Upon entering the lower level Batman catches a glimpse of the Scarecrow and several unfortunate victims of his fear gas trapped in an operating room. Soon he is affected by the gas himself, first subtly, then in increasingly surreal ways. He finds Gordon's dead body in an empty hallway and has a chilling encounter in the morgue with the reanimated corpses of his parents. The Dark Knight finds himself in a nightmarish dreamscape set in the crumbling ruins of Arkham Asylum, controlled by a gigantic, monstrous Scarecrow, whose fiery gaze he must evade until he can defeat him with a symbolic bat-signal.
Shaking off the effects of the fear gas, Batman awakes inside the Morgue. Batman leaves the Morgue and finds Scarecrow's gas had him believe something that wasn't real, finding a fallen security guard where he had seemingly found Gordon's corpse earlier. Batman realizes that Gordon is still alive and follows a trail left for him by the Joker to the scene of a vicious little game set up for him. Harley is guarding Gordon and Joker challenges Batman to make it undetected past four of his henchmen patrolling the room; if he is spotted Harley will execute Gordon instantly. Once Batman succeeds the Joker directs his attention to a surprise left for him in a previously locked chamber in the middle of the room.
Inside, he finds Bane, strung up in restraints and hooked up to a pump that's draining his Venom. He is the mysterious "Patient X" mentioned in the PR videos about Dr. Young's "Titan" project which were playing on some monitors in the Upper Corridor of the Medical Facility. The Joker triggers the pump, replacing Bane's Venom with Titan, which enables him to break free and attack Batman, hurling him through a wall and into the Medical Facility's Boiler Room. After a fierce battle Batman flees the Boiler Room by means of his grappling gun as the ceiling, weakened by the fight, collapses on Bane and buries him under a pile of rubble. Bane rises, however, from the debris to face Batman again, only to have the Dark Knight summon the Batmobile to the scene, ramming it directly into Bane and knocking him into the murky waters of the Gotham Bay.
Batman takes Commissioner Gordon to the docks in Arkham West, where an emergency launch is waiting to take the police commissioner back to the mainland. Gordon and a security guard get on the boat, leaving Batman standing alone on the docks.
After heading through a locked-up cave outside, Batman glides down to a secret Arkham-based sector of the Batcave which he installed beneath the island's surface years ago. Using the computer there he learns that Young has been researching the Venom drug fueling Bane and has managed to develop Titan, a similar, yet more powerful drug based on Bane's Venom, ostensibly intended to help inmates withstand the more... strenuous therapies. Realizing that Joker plans to use Titan for something sinister, Batman heads over to Arkham Mansion to reach Young's notes before the Joker gets there first.
With the help of the Batclaw, a gadget similar to the grappling gun that Batman assembled in the Arkham Batcave, Batman reaches the Old Sewer through the Arkham caves. He discovers the Joker has seized the tunnels of the Old Sewer and has posted several Blackgate convicts there to prevent him from proceeding. After defeating them Batman enters the Main Sewer Junction, which is a massive, crumbling, chamber with a maze of decrepit columns, archways, and platforms. He emerges from the Main Sewer Junction in the Surface Access area, which contains an unused exit to Arkham North. Here Batman finds that the Joker's men have gotten their hands on sniper rifles stolen from the guard armory. After being forced to deal with several of the armed convicts, Batman enters Arkham East only to find that the Joker had taken over this part of the island as well. Armed prisoners now guard the watch towers after having shot the security guards.
After being forced to contend with more gun-wielding thugs, Batman enters the Arkham Mansion through the air ventilation system. After defeating three of the Joker's men in the Entrance Hall, he fights his way through the Main Hall and enters the West Wing Corridor, where he rescues Arkham staff member Kevin Liew and an asylum guard. He notices 'Suicide Collars' worn by some of the Joker's henchmen, electronic devices that sound an alarm when they detect sudden heartbeat changes in the inmates. Batman then rescues Aaron Cash and another Arkham guard being held captive by a group of armed Blackgate convicts in the Records Room.
Batman eventually makes his way through the Mansion to Dr. Young's office, only to find that she has already retrieved the notes. He tracks a trail of her fingerprints to the mansion's library, where she hid the notes from the Joker. Briefly pausing to deal with several of the Joker's thugs and rescue Bill, a security guard, and an orderly being held captive, he destroys the notes. Unfortunately Joker had Zsasz kidnap Dr. Young herself and intends to have him torture the Titan formula out of her. While venturing through the Mansion to rescue Dr. Young, Batman is drugged by Scarecrow again, this time being forced to relive his parents' death, and having to battle past another giant Scarecrow. After emerging from the gas unharmed once more, he finds Zsasz holding Young hostage in Warden Sharp's office with a knife. He uses his Batarang to defeat Zsasz and rescue Young.
The shaken and harrowed Dr. Young reveals that Joker now has the Venom and her Titan formula. She talks of a laboratory inside the Botanical Gardens, but when she goes over to Sharp's safe to retrieve the security codes, she finds that the Joker had got there first and has rigged the safe with explosives. The blast kills Young, and Harley taunts a barely-conscious Batman with Warden Sharp, whom she is still holding hostage. After waking up completely and taking out the thugs Harley left behind, Batman tracks Harley to the Penitentiary.
Batman chases Harley through the building. He finds Sharp in the control room, frees him, and takes Sharp's security codes, enabling him to disable the electric barriers blocking his way with his Cryptographic Sequencer. At the same time, Harley releases Poison Ivy, whose cell Batman had passed earlier while she pleaded for his help, from captivity. To make matters worse, the Joker frees the rest of the crazed Arkham inmates. Batman follows Harley to a large room with an electrified floor, which she uses to try to kill him. When she fails, she sends her thugs after him. When they too fail Harley attacks Batman, but he successfully apprehends her and locks her in a cell. The Joker refuses to get her out of there and crosses her off his 'party list' for some kind of celebration he is holding later that night. Through a slip of the tongue from Harley, Batman learns that the Joker has a secret Titan production facility inside the Botanical Gardens.
Now in possession of the knowledge that Joker plans to build an army of Titan-fueled mutants (effectively an enormous group of Banes), Batman heads over to the Gardens and reaches the hidden laboratory. After battling two of the Joker's henchmen drugged with a now complete Titan serum, he destroys the facility and begins to search for an antidote to Titan. Since Titan is produced by genetically engineered plants (hence the location of the secret lab), Batman believes Poison Ivy could help him find a cure. Ivy refuses to help Batman (declaring that she'd rather watch him squirm) until he threatens to make every plant on Arkham suffer unless she cooperates. She informs him that the only way to create an antidote is to use some rare spores which can only be found in the sewers - directly inside the lair of Killer Croc.
As Batman leaves the Botanical Gardens, Joker announces that he has supplied the angered Ivy with some of the Titan serum. This causes her plants to grow to gigantic proportions, slowly covering the island and entangling its buildings while large, bulbous flowers appear everywhere that exude deadly spores.
After battling past Ivy's plants while heading back into Arkham Mansion, Batman learns from Aaron Cash that the only way to access Croc's lair is through a pathway in Intensive Treatment. After dealing with several of the Joker's "security guards" (inmate impostors wearing stolen guard jackets), Batman backtracks through the facility, but is drugged by the Scarecrow once more on his way through. Scarecrow injects an immense amount of toxins into him (enough to drive ten men insane), but when Batman still emerges triumphant, Scarecrow is shocked and flees into Croc's lair. Scarecrow dangles his toxins over the river in the pipeline, threatening to drop them in if Batman comes closer, which would affect the entire city of Gotham. As Scarecrow stands on the edge, Croc jumps out of the water and grabs him. Croc is about to eat Scarecrow, but Batman hits his shock collar with a Batarang, forcing him to recoil and drag Scarecrow into the water with him. Batman ventures into the sewers and, despite frequent attacks by Croc, gathers all of the required spores. As he prepares to exit the lair, Croc suddenly charges at him through a tunnel, but Batman destroys a weak part of the floor using his Explosive Gel just as Croc runs over it, sending him plummeting down into the river below.
Inside the Batcave, he uses the spores to create an antidote, and sets out to stop Ivy from taking over Arkham. While ascending back to the surface, Batman learns that Joker intends to contaminate Gotham's water supply with runoff from his Titan production. He foils this plan by disabling three pumping stations guarded by Joker's henchmen. He travels back to the Botanical Gardens, where Ivy states that while she originally thought that Titan was hurting her plants, it has actually made them much stronger. With that she summons a colossal Titan plant through the floor and bonds with it to fight Batman. She also sends waves of security guards infected by her mind-controlling plant spores out to fight Batman, including Eddie Burlow and William North. However, he manages to defeat her and the zombified guards, and Ivy and the plants sink back into the undergrowth. Upon emerging from the Gardens, Batman learns that the Joker's party is about to begin. He heads over to the Visitor Center, which has been recreated to match the Joker's style. The Blackgate prisoners announce Batman as the Joker's special guest and allow him entry.
Inside the Center, Batman is weakened when the Joker detonates a bomb on the other side of a thin glass window. He awakens to find Joker sitting on a throne of mannequins with Scarface sitting on his knee. The Joker sends some of his men along with two Titan-fueled policemen to attack Batman, and when they fail, he reveals Gordon tied up with some rope. Joker whips out a gun filled with Titan darts and takes a shot at Gordon, but Batman dives in the way and begins to mutate. When Batman resists the change, Joker declares that he is ruining his party, and, declaring he has nothing to live for, shoots himself through the lower jaw with the Titan gun.
The game flashes forwards to about 10 minutes later. News choppers are flying all around Arkham, cameras fixed on the roof of the Center. A horribly mutated Joker climbs up from inside the building, gripping Batman in his hands. Unlike all other Titan victims, Joker has kept his mind and is still taunting Batman to give in to the change. He tells him that he does not have long left. In retaliation, Batman injects himself with the antidote in order to prevent the Titan from taking control of him. Joker jumps up onto a high point and sends his men to attack Batman, but while he poses and shows off to the choppers, Batman yanks him down with the Batclaw and he crashes through the floorboards into an electrical circuit. He still climbs out, barely harmed at all, but as he brags about how he is victorious, Batman sprays Explosive Gel over his heavily armored knuckles. Stating that he will never let Joker win, he punches him in the face, detonating the Gel just as he does so, launching Joker backwards and knocking him unconscious.
Outside the Visitor Center, Gordon tells Batman that the effects of Titan are starting to wear off the Joker and his men, and that they are being taken back to their cells. The Medical Facility is being used as a makeshift hospital for the injured Arkham staff. At that moment, Batman is informed that Two-Face is raiding a bank in Gotham City, and flies away into the night in the Batwing.
After the credits roll, a crate marked 'Titan' is seen floating through the sea outside Arkham. A appearance Scarecrow, grabs the crate, as the villain is still at large.