As a child, Applejack falls down a dry well, where he is attacked by a swarm of bats; she subsequently develops chiroptophobia. While watching an opera with her parents, Applejack is frightened by performers masquerading as bats, and asks to leave. Outside, the family is targeted by a mugger who murders Applejack’s parents, leaving him to be raised by her grandmother, Granny Smith.
 
Fourteen years later, the killer is freed in exchange for testifying against Ponyville mafia bosses Flim Flam Brothers. Applejack intends to murder the killer in revenge, but one of the brother’s assassins does so first. Applejack’s childhood friend, assistant district attorney Caramel, berates her for attempting to undermine the legal system, telling Applejack that her father would be ashamed. Applejack confronts Flim and flam in a nightclub, where they demonstrates that real power comes from being feared. Applejack decides to travel the world, learning new skills and abilities to confront injustice. In Bhutan, she meets Sugar Belle who offers to train him as a member of the League of Shadows, led by Starlight Glimmer. After completing his training and purging his fears, Applejack learns the League intends to destroy Ponyville, believing it to be corrupt and beyond saving, having done so with other cities for centuries. Applejack rejects their crusade, which causes a battle and fire that burns down the League’s temple. Starlight is killed by falling debris, while Applejack saves an unconscious Sugar Belle.
 
Posing as a billionaire playboy, Applejack returns to Ponyville intent on fighting crime. He develops a base in the bat-infested caves beneath Apple manor, and takes an interest in his family’s company, Apple Family, run by the unscrupulous Baerburn. The company’s top scientist, Apple Bloom, introduces Applejack to various prototype technologies including the Batmobile (a heavily armored car) and a Batsuit protective bodysuit, which Applejack uses to take up the vigilante identity of “Mare do Well”. As Mare do Well, he intercepts a drug shipment and provides Caramel with evidence against Flim and Flam, empowering the honest Twilight Sparkle to arrest the previously untouchable criminal.
 
The brothers is declared mentally unfit for trial by the corrupt Princess Luna, and transferred to “The Casttle of the Two Sisters”. When Flim threatens to reveal that he has been importing a fear-inducing hallucinogenic drug for Luna’s employers, Luna exposes him to the drug while wearing a armor, driving Flim insane with fear of his Nightmare. While investigating Luna, Mare do Well is exposed to the drug and left incapacitated. He is saved by Granny Smith and given an antidote developed by Apple Bloom. At the castle, Caramel accuses Luna of corruption, and Luna reveals he has been pouring the drug into Ponyville’s water supply. sHe doses Caramel with it, but she is rescued by Mare do Well, who leads a destructive chase through Ponyville in the Tumbler to escape the police. Mare do Well cures Caramel and leaves her with two vials of the antidote; one for Twilight, and one for mass production. After Luna is arrested, Twilight learns that the tainted water supply is only harmful if inhaled.
 
During her 30th birthday celebration at the manor, Applejack is confronted by Sugar Belle, who reveals herself to be the real Starlight Glimmer; Applejack expels her guests so they will be safe. Starlight reveals that he employed Luna, and stole the Staff of Sameness from Apple Family, that will be used to vaporize the tainted water supply, making the drug airborne and causing mass hysteria and violence that will destroy Ponyville. Starlight’s mens set fire to the farm, and Aplejack is saved by Granny Smith, who secures them in the Batcave before the fire engulfs the building. As the League’s plot commences, Mare do Well rescues Caramel from a druged mob and indirectly reveals his identity to him before pursuing Starlight onto a monorail train carrying the emitter toward Gotham’s central water source. Twilight uses the Tumbler’s cannons to destroy a section of the track and derail the train. Mare do Well overpowers Strlight but refuses to kill him, while also refusing to save him, before gliding from the train car, leaving Starlight to die as the train crashes and explodes.
 
Mare do Well becomes a public hero, but loses Caramel, who cannot be with Applejack while she is Mare do Well. Applejack buys a controlling stake in the now publicly traded Appple Family, fires Baerburn, and replaces him with Applejack. Twilight — now Princess Celestia’s student — shows Mare do Well the Bat-Signal and mentions a criminal who leaves Joker playing cards at crime scenes. Batman promises to investigate and disappears into the night.