Batman: Vengeance

Setting

Based on most of the game's character designs and appearances, Batman Vengeance would seem to take place after the conclusion of Batman: The Animated Series, but before the start of The New Batman Adventures. Plot points that support this include Mr. Freeze still posing as a threat (as his appearance in The New Batman Adventures episode "Cold Comfort" was the last time he was seen prior to Batman Beyond), as well as the fact that Batgirl is the Dark Knight's only active sidekick in the game.

Batman by this point is well established as the guardian of Gotham City, with the game sharing the voice cast, production design, and continuity of the DC animated universe. During the course of the game, Batman is monitored and assisted by Batgirl in the Batcave.

Plot

After saving the life of a woman named Mary Flynn from an apparent attempted murder at the hands of the Joker at Gotham Chemical, which resulted in the complex blowing up due to a ticking time bomb left next to a tied up Mary by the Joker, Batman investigates what possible interest his nemesis would have in the woman. He learns that Joker had abducted her son, Toby, and is holding him for a $5 million ransom and will kill both Mary and her son if she does not pay up soon, implying that Mary has high financial access. After Mary is abducted by Joker's gang for the second time, Batman traces her location, using a tracker he previously gave to her, to a partially demolished Gotham bridge, where he comes face-to-face with the Joker once more. As the Joker seems to throw Mary's son off the remains of the bridge, the Dark Knight saves the boy before it's revealed to be a dummy, and Mary reveals herself to be the Joker's companion Harley Quinn; Toby was never real and the abduction was merely a farce to lure Batman into a trap. Batman then engages the Joker and defeats him, but in the fray, the villain falls off the bridge and to his apparent death. After saving Harley from attempting suicide by jumping off the bridge, Batman lets a distraught Quinn go and monitors her activities, knowing that the Joker is most likely not dead and Harley could be his only opportunity to learn more of the Clown Prince of Crime's true plans, making her a more valuable asset on the outside than she would be incarcerated.

As Batman continues to keep tabs over Harley, he is alerted to a crisis at a pharmaceutical company, Gotham Industrial, which is under attack by Mr. Freeze, who is angrily searching the complex for a scientist named Isaac Evers, whom he believes sent him a promotional video for a drug developed by Evers, known as Promethium, for treating conditions on the cryogenically frozen. Freeze had apparently used the drug on himself and his wife, Nora, but to no avail, infuriating Freeze with the implication that Evers had sent him the tape to taunt him. After finding Evers, Freeze abducts him and escapes the complex in a helicopter. Batman gives chase in the Batwing and eventually rescues Evers, who explains his work and what Freeze was after, lying to Batman by telling him the source of his funding originates from a grant supplied by the Wayne foundation. Knowing this to be a lie, Batman tells Evers to go into hiding, and later returns to Gotham Industrial to learn more about the source of Issac's financial backing, eventually learning that the scientist had his funding pulled, due to Promethium being far too unstable, as it contains several flammable particles. Evers was able to successfully continue in his research after receiving funding from the Joker, with every rise in Evers' budget coinciding with a successful bank heist of Joker's doing, implying the villain had plans of his own for the drug. Freeze and his gang then attack the facility again to find Isaac, destroying most of Ever's lab in the process, but are eventually stopped by the Dark Knight, with Freeze encased in ice from his own freeze gun.

Meanwhile, Batgirl traces the transmitter, previously given to Harley Quinn by Batman when he believed her to be Mary Flynn, and finds it on Gotham's mayor, Hamilton Hill, who is seen making a deal with a mysterious and large man in a trench coat. Batgirl tracks the man to a metro train, but is discovered and attacked as Batman races to assist. As Batman reaches Batgirl and her attacker, the man jumps off the train and tears away in a stolen car. Batman and Batgirl pursue their suspect in the Batmobile, and cause it to crash off a highway outside the city. Batman investigates the wreckage, but discovers the man got away and finds only an apple outside the wreckage.

Back at the Batcave, Batgirl examines the apple found at the crash and discovers a live plant inside, coming to the conclusion that Poison Ivy had implanted such a creature inside the mayor and is blackmailing him for money and power. Batman's surveillance of Mayor Hill leads him back to Gotham Chemical, where he confronts the trench-coated thug, who is revealed to be a plant creature created by Poison Ivy, and knocks the creature into a vat of acid. It is revealed that, earlier during the night, an unseen individual had left Poison Ivy a mysterious substance that was previously manufactured at Gotham Chemical, prior to its destruction at Joker's hands. Upon further examination of the chemical, Ivy discovered unique particles that, when exposed to any type of plant life, transforms plants into truly sentient and vicious creatures. Using this to her advantage, Ivy manipulatively plants several of her upgraded plants inside powerful politicians and businessmen through apples and other foods, blackmailing them for money, power, and even environmental donations. Knowing the origin of the chemical, Ivy had her plants rebuild Gotham Chemical in an effort to produce more of the chemical and created an antidote to the condition the mayor and the others have to use as collateral to ensure that they follow through on their deals. Harley had placed the transmitter on Mayor Hill, when he was receiving some of the plant food that would temporarily keep the creature at bay, in an effort to alert Batman towards Ivy's activities and ultimately stop her from going too far in her schemes after she came to her for assistance with Gotham Chemical.

After Batman defeats Poison Ivy by electrocuting all of her plants, obtaining the cure, and saving Mayor Hill and the victims of Ivy's schemes, he heads to Funnibones Warehouse, after witnessing Joker's men hijack a blimp from the Gotham Air Strip, to collect from Harley for letting her walk the night the Joker was apparently killed. She informs him that, with Joker gone, some of his men were still operating on their own and left with some of the villain's toys and the blueprints to the historic Gotham Gasworks. Upon arriving at the Gasworks, Batman discovers Joker's men sending the villain's flammable toys into the pipe network, which lead throughout the entire city, and opens the gates to the sprinkler system to flood the complex's pipes in order to stop the toys. After disarming the last of Joker's men, Batman finds a tied up Isaac Evers, the apparent mastermind behind the Gasworks plot, who claims he only wanted to burn down Gotham Industrial in order to collect on the insurance money, as he couldn't collect on the damage left by Freeze without revealing his financial backers, particularly the Joker. With the Harlequin of Hate having funded the research with filthy lucre, Evers would be arrested for criminal facilitation and conspiracy if he revealed his affiliation with the notorious criminal and resorted to hiring the Joker's men and using his equipment in order to throw the cops off his trail after burning down his business, but the gang eventually turned on him, tied him up, and embarked on their own agenda of sending the toys throughout the city. The Dark Knight takes Evers outside for the arriving Gotham Police to take him into custody, but is forced to go undercover after being framed for injuring Commissioner Gordon with a Batarang, which led to a SWAT chase around Gotham City.

Injured and hunted by the police, Batman's investigations shift towards discovering who framed him and how everything that has occurred since the Joker's disappearance factor together. He ultimately heads back to Funnibones Warehouse, disguised, for more information, only to discover the knife that the Joker was holding the night he fell from the bridge, confirming the Joker is not dead. Batman realizes, that with the Joker's plans occurring over such a long period of time, his end goal was massive and threatens to destroy the entire city. The Harlequin of Hate finally resurfaces on the roof of the Gotham Gasworks with the stolen blimp and his gang, where he reveals that he was behind the entire crime wave that occurred after faking his death by subtly manipulating the other villains and using Isaac Evers' research, having worked with the scientist and funded all his experiments and operations through his ill-conceived fortune, to produce large quantities of the highly flammable Promethium. Weeks earlier, the Joker had arranged the fake kidnapping scheme to fake his own death in order to reside in the shadows and out of the police and Batman's scope, while he manipulated the other villains; he sent Mr. Freeze the promotional tape on Promethium to provoke him into attacking Isaac's lair so his men could convince Evers to hire their services in an insurance scam with the use of Gotham Gasworks, provided Poison Ivy with the plant enhancement chemical and used her schemes to rebuild Gotham Chemical to mass-produce his own signature Joker toxin in a quiet fashion without Batman noticing, and finally used Harley to relay false information to Batman to send him deeper into his plot at the Gasworks and ultimately frame him for attacking Commissioner Gordon.

Using Evers as a scapegoat for the Gasworks scheme, the Joker reveals that he manipulated Batman into opening up the pipes to the sprinkler system, which the Joker then plans to pump with his Joker toxin, mixed with Evers' altered drug to make it highly flammable, all over the city through a feed tube connected to the previously stolen blimp, now filled with the deadly compound, and burn the city to the ground, while its citizen choke to death on their own laughter. The villain's ultimate 'joke' is that Gotham would be completely destroyed, with the punchline being Batman had been unknowingly aiding due to the Joker's manipulation. The Clown Prince of Crime then prepares to escape in the blimp and watch Gotham from above become engulfed in flames and toxin, leaving groups of his men, armed with explosives and flamethrowers, to slow the hero down. Despite this, Batman manages to shut down the gas flow, defeat all of the Joker's thugs, and subdue Harley Quinn just in time to get on the Joker's blimp before it takes to the sky. Despite having stopped the flow of Promethium and Joker toxin into the sprinkler system, Joker plans to use the remaining compound stored in the blimp to destroy the city by setting the blimp on a collision course with the heart of Gotham, City Hall, to explosively release the compound into the air. After a brief fight with the Joker, Batman knocks the villain out, deteriorates the gas, and disables the auto-pilot after solving a mechanism created by the Ace of Knaves to protect the auto-pilot controls. Once he realizes all his plans have failed, the Clown Prince of Crime decides to play one last, twisted joke on Batman and jumps from the blimp to entice the Dark Knight to save him and have a final showdown, while plummeting down to Gotham. The Dark Knight manages to both defeat and save the Joker and destroys the blimp, finally taking his archenemy back to Arkham Asylum.

Commissioner Gordon calls Batman to apologize for the earlier SWAT chase, as they found Harley's fingerprints on the Batarang that hit him. As Mr. Freeze, Poison Ivy, Harley and the Joker sit in Arkham Asylum, Batman looks out over the city as the Bat-Signal ignites on him.