As a child, Chris Wolff had been diagnosed with a high-functioning form of autism and was offered an opportunity to live at Harbor Neuroscience Institute in New Hampshire. Although Chris had bonded with Justine (Alison Wright), the mute daughter of the institute's director, his father declined, believing that Chris should overcome the hardships inherent in his condition. The pressure of raising a special-needs child later drove Chris's mother to leave him and his neurotypical younger brother, Braxton. Their overbearing father, an army psychological warfare officer, arranged for them to receive extensive military training around the world, which Christian now uses to protect himself in his dangerous life.
Now an adult, Chris (Ben Affleck), a hapless mental calculator, works as a forensic accountant, tracking insider financial deceptions for numerous criminal enterprises. His clients are brokered to him via phone by an unidentified woman's voice, which originates from a restricted number. As an auditor of criminal enterprises, he accepts payment both in cash and in various non-cash forms such as rare comics, gold bricks, and paintings by famous artists. Pursuing him is Ray King (J.K. Simmons), the director of FinCEN in the Treasury Department, who recognizes Chris by the alias "The Accountant". King blackmails young data analyst Marybeth Medina (Cynthia Addai-Robinson) into helping him identify and arrest the Accountant prior to his retirement, threatening to expose her undeclared criminal past (for the felony of lying on a federal employment application) if she refuses. King's only leads are Chris' numerous cover names.
The voice gives Chris his latest assignment, auditing robotics corporation Living Robotics, whose in-house accountant, Dana Cummings (Anna Kendrick), has found suspicious financial discrepancies. The company's founder and CEO, Lamar Blackburn (John Lithgow), and his sister and associate Rita (Jean Smart) willingly cooperate with Chris' investigation, while CFO Ed Chilton (Andy Umberger) dismisses Dana's findings as a mistake. However, after Dana provides him the company's records, Chris quickly discovers that over $61 million has been embezzled from the company. The following night, Chilton, who is diabetic, is confronted in his home by a hitman (Jon Bernthal), who forces him to self-administer a fatal insulin overdose. Later, Lamar surmises to Chris that Chilton embezzled the money and was driven to suicide out of guilt. Upset by Chilton's death, Lamar closes the investigation, leaving Chris distraught from unfinished work.
Meanwhile, Medina realizes Chris's cover identities, including his current name, are all famous mathematicians (Carl Gauss, Lou Carroll, and Christian Wolff). Using facial recognition to track the Accountant leads her to a shootout in which several members of the Gambino crime family had been killed. Analyzing a sound recording, Medina isolates Chris' voice, determining that he is muttering the nursery rhyme Solomon Grundy to himself, a behavior consistent with autism spectrum disorder. The trail leads her to the modest accounting office that Chris uses as a cover: ZZZ Accounting, in Plainfield, Illinois, dividing his profits through four cash-only businesses in his block. She learns that Chris has written off hefty tax returns with donations to the Harbor Neuroscience Institute.
Chris and Dana are targeted for assassination, but Chris, having retained the skills taught to him by his father to protect himself in his dangerous life, kills his own pursuers and rescues Dana, taking her to the trailer where he keeps the only things he values, including an original Jackson Pollock painting among his non-cash payments. While in hiding, they realize that the embezzled money was reinvested in affiliated companies in order to raise Living Robotics' stock price. Concluding that Rita is behind everything, Chris goes to her house, only to find her dead, murdered by the hitman, who escapes just as Chris is arriving. Thus, Lamar is exposed as the real mastermind.
King and Medina arrive at Chris' house and find evidence (cameras hidden in bird houses and an M134 minigun in the garage) that he is the Accountant. King reveals that Chris had been arrested after he started a melee at his remarried mother's funeral that led to his father's death, taking a deputy's bullet meant for Chris. In jail, Chris had been mentored by Francis Silverberg (Jeffrey Tambor), a former accountant and fixer for the Gambino crime family, who subsequently became an informant for the United States government. Silverberg was later released and tortured to death by the Gambino family, which drove an enraged Chris to escape from jail and exact revenge on the people responsible.
King confides to Medina that he was present at the shootout and that Chris spared his life after questioning him about being a "good dad". Afterwards, King had been contacted by the voice and provided with evidence Chris had compiled on criminals who violated his moral code, helping King rise to his position of director. King tells Medina that her investigation of the Accountant has been a test, and she has been selected to replace King, after his retirement, as the voice's contact in the Treasury Department.
Chris attacks Lamar's mansion and kills the mercenary guards led by the hitman. After a shootout, the hitman recognizes the nursery rhyme that Chris mutters to himself as he tends to his wounds. He confronts Chris and reveals himself to be Braxton, who had become estranged after their mother's funeral. Still resentful towards their mother for leaving, Braxton blames Chris for getting their father killed. The two reconcile after a hand-to-hand fight, and Lamar shows himself to chastise Chris. After Chris proceeds to kill Lamar without objection from Braxton, the two amiably agree to meet up another time. Later, the voice relays Chris's evidence on Lamar's criminal activities to Medina, who has accepted King's offer, and she dismantles Living Robotics. Chris then bids farewell to Dana by sending her the Pollock (covered up by the painting Dogs Playing Poker, a reference to their initial conversation), and leaves to find Braxton.
In a scene at the Harbor Neuroscience Institute, the voice is revealed to be a computer-generated voice from a powerful computer, given to the Institute as a donation by Chris. The computer is used by a (still mute) adult Justine to communicate, and also fulfill her duties as Chris' partner.
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