The film begins with a man walking through a bar with multiple dead bodies on the ground, having been shot in the head. He slowly makes his way upstairs, hearing someone begging for his life. He passes more bodies, making his way to the door of the room where the begging man is. An abrupt sound is heard and the begging stops. The next scene takes place about 30 years ago (via title card) at a place called the Harbor Neuroscience Institute in New Hampshire.
It's a big, beautiful home in a forested area. Two young boys are sitting in a living room. One is sitting calmly in a chair, and the other unboxes a puzzle and rapidly starts putting it together. The boy with the puzzle is shaking and murmuring to himself.
A young girl is also in the room with a caregiver who is trying to put her shoes on. The young girl screams and smacks her own head and is unable to communicate. The boy quickly assembles the puzzle but starts screaming inconsolably when one piece is missing, repeating over and over that he has to finish the puzzle. The young girl has stopped screaming and reaches over to pick up the piece that had fallen under the table and hands it to the young boy, and they look directly at each other.
The boy completes the puzzle, revealing that he has assembled it upside down, without seeing the image of Muhammed Ali to guide him. In the adjacent room, a psychologist is speaking to the parents of the two boys. There is a sign on the refrigerator with simple drawings of six stick figure faces, happy, angry, sad, etc. They discuss the puzzle boy's sensitivity to bright light and loud noises. He is also stubborn and fixates on things, like wearing only one t-shirt, which the psychologist explains is due to a tactile sensitivity. He is also likely to channel his anxiety into repetitive behaviors like shaking, tapping his fingers and talking to himself. He tells them that the boy will likely always have problem with things like maintaining eye contact or making friends.
The mother explains that the father is in the military, which means they move frequently, so the boy hasn't been able to make friends anyway, leaving his younger brother as the only friend he has. The father seems uninterested in the conversation. The psychologist suggests that they leave the boy at his institute, where they can teach him coping mechanisms and provide a calm, comforting environment that won't exacerbate his sensitivities. The father says no, telling the psychologist that if the boy is sensitive to light and sound, he needs to be exposed to more light and sound, as the world is not going to accommodate his special needs. In the present day, Christian Wolff (Ben Affleck) is an accountant in his own, small practice.
He has a few small tics, like tapping his fingers on the desk or blowing on them quickly. He has a very flat affect when speaking, and he doesn't seem very warm or friendly. He is meeting with a farmer and his wife. The farmer is embarrassed that they have fallen on tough times, and his wife gently suggests that they pay their taxes via credit card to buy some more time.
She sees Christian seemingly staring at her necklace and asks if he likes it as she made it herself. He responds in a monotone, direct way and says he doesn't like it, but asks if she sells any jewelry she makes. She tells him that she just sells a few at church fairs or to friends but not in any meaningful way. He asks if she has an office she uses to produce her wares, and she keeps insisting that it's just a hobby she does when she's watching TV. He is gently steering them toward declaring it as a home business, telling them the IRS allows the deduction of a certain amount of household expenses when used for business purposes. He subtly suggests to the husband that they declare a large portion of the house as her "home office. " After more questioning, she says she simply drives her truck to the local craft store to purchase beads, and he corrects her, saying she is driving the company vehicle to purchase business supplies.
The farmer and his wife leave in a much happier mood, grateful to Christian for his expertise. The farmer invites Christian to his home for fishing, to which Christian responds flatly that he doesn't fish, but he does shoot. The farmer tells him he has plenty of space for shooting if he'd like to visit them sometime. Christian does visit the farm and sets up cantaloupes with simple faces drawn on, matching the stick figure faces seen in the Harbor Institute.
He sets up with a high powered sniper rifle. The farmer watches through binoculars from the house and claims that the 1,000 foot distance would be impossible for Christian to hit, but Christian shoots them all accurately in quick succession. Meanwhile, Ray King (JR Simmons), the director of financial crimes at the Treasury Department calls a young analyst, Marybeth Medina, into his office. He credits her with a big investigation, though she demurs and says it was a team effort. He asks why she hasn't applied for an agent position, and she deflects, saying she enjoys her job.
Ray shows her what he has on his computer screen, which is Marybeth's juvenile criminal record. It shows serious charges including assault, drugs and attempted murder. She is shocked as she believed the records to be sealed. He tells her that it's a felony offense to lie on an application to work for the federal government, as she had hidden her past.
She asks what he wants. Ray hands her a stack of photographs, which show terrorists, drug cartel leaders, mafia bosses, and other criminal leaders meeting with the same man, who is only seen from behind or partial profile. Ray explains that he is an accountant who works for the world's biggest criminals, as they cannot call H&R Block when they have a financial problem. He is surprised that the accountant has survived this long, given how dangerous his clientele is. He knows of multiple aliases used by the accountant, including Lou Carroll and Carl Gauss. Ray tells Marybeth that he is retiring soon, and her job is to find out who the accountant is, or he will reveal her criminal past. In Zurich, a man gets into his car in a parking garage. A second man (the Assassin) quickly enters the vehicle and calmly pulls out his gun, placing a silencer on it.
The first man is dismissive, saying he has kidnapping insurance so the Assassin should just get on with his business quickly. The Assassin is surprised at his arrogance. He explains that he was hired to send a message to the man, who is a stockbroker and has been shorting the stocks of the Assassin's boss' company. The Assassin orders the stockbroker to stop shorting stocks.
The man is continually arrogant and dismissive, so the Assassin strikes him deftly and repeatedly. The man tries reaching for the gun at one point, but the Assassin skillfully deflects him. The man finally submits and asks which company he should stop shorting, as he does it to many companies. The Assassin simply tells him to stop shorting all stocks or he'll return to kill him. He exits the car and leaves.
Christian drives to his home, which is very bare. He has no art or photos or any decorations in the house. He owns exactly one plate, one fork, one knife, one spoon, and prepares himself dinner. He is highly ritualized in the way he prepares his food. He continuously shows small tics, like blowing on his fingers before picking up his fork.
Later in the evening, he goes into his bedroom and turns on a strobe light and loud, heavy metal music. He picks up a small, wooden rod and uses it to roll on his leg muscles. He is trying to remain calm, subjecting himself to the stressful stimuli until his alarm beeps and it's time to take his Zoloft. Interspersed throughout the film are flashbacks to Christian's childhood. One day his mother leaves their family, as the stress of taking care of the boys, particularly with special needs, is unbearable as the father is never around. Young Christian is screaming and throwing things and punching through walls, while his younger brother watches resentfully. The father is arguing with the mother that she can't abandon her family and tells her to wait a moment. He runs in the house to hold Christian tightly until he calms down.
The mother gets into her waiting cab, and the younger brother gives her the middle finger from the window. In present day, Christian is seen talking on the phone with a woman (the Voice) whose caller ID is a smiley face, similar to the ones from the stick figure face diagram referenced earlier. She has a very flat affect as well and is prone to stating emotions or describing her behavior, such as stating "deep sigh" rather than actually sighing. They are discussing new jobs for Christian.
She suggests he take a legitimate job for a company called Living Robotics rather than a criminal assignment that is more dangerous, as she cares for his safety. They also discuss some of his assets, including a Renoir painting and a Pollock painting, that she is trying to sell for him. Christian drives to a storage facility where he keeps a trailer. Inside are his valuable paintings as well as cash, passports, gold bullion, first edition comic books and a storage space for lots of serious weapons. He also has a copy of the stick figure face diagram. He checks on everything periodically and goes on his way.
Marybeth's investigation continues, and she is able to figure out that the Accountant's known aliases are actually a famous mathematician (Carl Gauss) and Lewis Carroll, the author of Alice in Wonderland who was also a mathematician and suspected of having Asperger's. She relies on friends in the FBI who use the profile pictures to assemble a suggestion of what his face might look like. They are also able to connect it to an unknown man who attacked a bar/club that was the base of operations for the Gambino crime family. The man killed the two guards standing outside and then entered the home, killing the seven people inside using their own weapons, including the mafia boss' son, Little Nicky, who was killed with one swift kick to the head. The house was bugged, as the family was being investigated, so there is an audio recording of the attack, including a man begging for his life (linking it to the opening scene). Nothing else can be heard other than the man begging and then the kick.
Marybeth manipulates the audio file and is eventually able to isolate a second, very quiet voice that seems to be muttering something repeatedly. She sends this file to experts who tell her that it is a nursery rhyme being repeated over and over again. She explains that the recording was made during a highly-stressful event, which makes the expert ask if the person was traumatized as young child. The flat affect and repetitive nature of the recording, despite a high-stress environment, would indicate that the person has some sort of neurological disorder, such as autism. Another flashback to Christian's childhood shows that the family is living in Indonesia. An older man is teaching the boys to fight and is quite brutal in beating them. The father watches from the side while casually reading a newspaper. The instructor finally says that they are just boys and that's enough training.
The father remarks that if they were done, the instructor would be laying on the ground bleeding. Young Christian replies in Indonesian that the instructor should continue. The younger brother is deeply loyal to Christian, though he seems exhausted from the fight as well. Christian visits Living Robotics where he meets with the CFO and the CEO's sister, who is a high-ranking executive of the company. The CFO is clearly put off that an outside financial consultant has been brought in to figure out a major financial discrepancy in the books. He says that a young accountant who didn't know what she was doing stuck her nose into things that weren't her business. He says he's been working with the CEO, Lamar, for 15 years and would never hurt the company.
He also claims that the company's records would be far too complex for Christian to decipher as they manufacture over 100 different products and have three different businesses. Christian brushes off his concerns and asks for the documents to be prepared for him. Christian also meets with Lamar, the CEO, who tells him that he (Christian) came highly recommended by someone whose daughter needed the company's advanced prosthetics. Lamar gives him a tour, showing him how their prosthetics have helped the lives of many amputees. Lamar promises to fully cooperate with Christian's investigation and to give him whatever he needs to complete the job. The next day Christian returns to Living Robotics to find a young woman asleep in the conference room with boxes of files and folders neatly prepared for him. He wakes her and she introduces herself as Dana Cummings (Anna Kendrick), the in-house accountant who found the discrepancies. She tries to offer her assistance to walk him through the files and suggests they have lunch together.
Christian, in his somewhat odd demeanor, turns down her offer. He sets about his work, which is highly ritualized. He goes through all the old files and begins writing on the whiteboards and then on the windows of the conference room. He takes a break for lunch and happens to sit near Dana who is also eating her lunch outside. She notices his dented, steel thermos, and she tries to make small talk with him about why he went into financial consulting. She tries joking with Christian, who is polite but doesn't get jokes.
She tells him that she wanted to study art, but her father discouraged this and told her to follow in his footsteps as an accountant, the kind with a nerdy pocket protector, which Christian is also wearing. She tells him the only art her father likes is dogs playing poker, which Christian says he also likes. Christian works through the night and is able to deduce that $61 million is missing from the company. He starts to explain it to Dana who catches on quickly. The CEO's sister interrupts them and dismisses Dana. She wants to know if Christian has guessed who's responsible for the missing money, to which Christian responds that he doesn't guess. He needs to keep reviewing the documents to figure it out. She expects a full report from him shortly.
That night, the CFO of Living Robotics wakes up when he hears a noise downstairs. He heads down and finds the Assassin waiting in his kitchen, with two henchmen. They sit together and the Assassin calmly tells the CFO he should give himself a double dose of insulin, so his death will appear like an accident. Otherwise, they will kill him violently and there might be a struggle, waking his wife, and they would have to kill her too and stage it as a robbery. The CFO tearfully agrees. The next day, Christian arrives at the office of Living Robotics to see all the files being packed up and his work being erased.
He is distraught at being unable to finish his investigation. Lamar, the CEO, is upset, believing that his friend, the CFO, killed himself as he had been giving himself injections for many years and wouldn't have made such a simple mistake. Lamar tells Christian that the CFO killed himself out of guilt for scamming the money, and Lamar says his friend was more important than the money. That night Christian engages in his usual ritual with the strobe light and loud music, but he is deeply frustrated that he wasn't able to finish his assignment.
He hits himself painfully with his wooden rod and is unable to cope with the stimuli. He grabs his medication and forcefully throws it across the room before calming down and picking it up. Another flashback shows Christian in prison, talking with an older man with glasses (Jeffrey Tambor). The man is very kind to Christian and is trying to coach him in having normal interactions with people, learning to read their emotions from the tone of their voice and their facial expressions.
They share a bunk, and late at night, he tells Christian about his clients, who are the criminals mentioned in the beginning of the film. Christian visits the farmer and his wife again, to practice more shooting. As he sets up, he has a flashback to another childhood memory when his family was living in France. His father drives him and his brother to an abandoned alley where four teens are hanging around. The teens have been bullying Christian, and his father tells him that he must fight back as people will walk all over him otherwise.
Christian gets out of the car and runs up to the bigger teens, beating them up. The younger brother waits in the car, until his father tells him to follow, and he leaps out of the car to help Christian. The Assassin's two henchmen have followed Christian to the farm and are holding the farmer and his wife inside hostage. They have the wife call out to Christian, but he doesn't seem to hear them. Then suddenly, one of the henchmen is shot through the head by a sniper rifle. The other henchman grabs the couple and heads to the car, but Christian shoots out the tires.
He then heads to the couple's truck, and Christian shoots the engine to disable it. He runs up to the truck and grabs the henchman. Christian strangles him and asks who hired him. The henchman won't say, but hands over Dana's ID, saying that his instructions were to kill the two of them. Christian kills him and casually waves bye to the farmer and his wife. Christian rushes out in his truck and calls the Voice. She tells him to get to his storage unit, hitch up the trailer and get out of town immediately, in her flat affect. She works on setting up a new identity, changing the registration on his car, and killing off the Christian Wolff identity.
She advises him not to worry about Dana, as he only has time to save himself. Marybeth's investigation leads her to a friend at the IRS. He helps her comb through tax returns of accountants with the names of Carl Gauss and Lewis Caroll. Using some filters, they narrow down the list but the most likely suspects are already dead.
She then produces a list of 100 of the most famous mathematicians, believing that the Accountant would be using the list as his aliases. They slowly search through the system for the different names. Christian goes to Dana's apartment, afraid for her safety. He sees that she is being followed by somebody through the window but can't enter the building. He gets in through a service entrance and climbs the stairs rapidly to get to her floor. Two delivery men have followed her down her hallway, though she doesn't suspect anything. Two more guards are waiting in the hallway.
Christian quickly kills the two guards in the hallway. The two delivery men burst into Dana's apartment, attacking her but she fights back. She locks herself in the bathroom and tries to escape. Christian enters, killing one of the men and then fighting the other man who has just broken into the bathroom. Dana is shocked to see Christian who has ruthlessly dispatched the men.
Christian takes Dana with him to his storage unit. He instructs her to wait outside but she enters anyway, finding his cash and valuable paintings and a storage space his weapons. He is annoyed that she came inside to his private space where he is packing up clothes, cash, passports and comic books. She questions how he owns an original Renoir and an original Pollock, which he explains he received as payment.
Marybeth's exhaustive search has not yielded anything so far. On a hunch, they pull up the two accountants who fit her profile (Caucasian male, age 25-45) for the last name on the list, Christian Wolff. One declared an income of over $500,000, which tipped the IRS off for an audit, which revealed that he was clean. The other declared an income of $75,000. This accountant's firm is called ZZZ Accounting, which seems suspicious as it's a bad choice for a name when they are listed alphabetically in a phone book. They look up a picture of the street view for the firm, which is in a dingy strip mall with a nail salon, laundromat and Chinese food restaurant. On a hunch, Marybeth has her friend look up the tax returns on the three neighboring businesses. ZZZ Accounting is listed as the accountant for all three businesses, who have each declared over $400,000 in income.
When they try to figure out where the money has gone, they realize that huge charitable contributions have been made to Harbor Neuroscience. Marybeth takes this information to Ray who is speaking at a press conference about a recent high-profile investigation that was completed successfully. When questioned about how they received such intel, Ray simply cites good old-fashioned investigative work. Marybeth shows him her research and they agree to check out ZZZ Accounting and Christian Wolff. Christian takes Dana to a fancy hotel. They talk more about the strange accounts of Living Robotics. Christian uncovered that $61 million was embezzled but then hidden under different accounts, so it wasn't technically missing. They go up to their room, and Christian paces around the hotel room, muttering something over and over to himself, so Dana asks him to sit with her.
They talk, and Christian tells her that he has high-functioning autism, so he has difficulty connecting with people even though he wants to. Dana tells him a story of how she wanted to buy an expensive gown for her high school prom so that she could wow her classmates and feel like she deserved to be special and to belong, forming a connection with Christian. Her original plan backfired when she tried to learn to count cards and go to a casino with all her savings, but on her way out with her remaining $20, she played a slot machine and won enough money to buy the dress, which she only wore one time. She asks Christian why he brought them to a fancy hotel to hide out, which he deflects by saying the water pressure is good. He then cites the nice towels, as he wanted her to enjoy it. She starts to lean in and get closer to Christian, when he suddenly sits up and references an old electronics chain.
He remembers it because the business owner ran an ingenious scam by stealing money out of the business but then investing it back in it, inflating its value so that its stocks would sell for more money. He realizes this is what Living Robotics must be doing. Christian sets out to see Lamar's sister, believing her to be behind the plot. As he pulls up to her home, he sees a suspicious man exiting her building.
He follows from across the street, and we see that it's the Assassin. The Assassin seems to know someone is following him though he never turns and looks. He then quickly pulls out his gun and fires two shots at Christian, who ducks behind a car. When he peers out, the Assassin is gone. Christian enters the building and finds that Lamar's sister is dead. Marybeth and Ray are able to track down Christian's home, which he has abandoned. They find high-tech surveillance cameras outside as well as a huge machine gun mounted in his garage.
Ray sees the dented thermos in the cupboard and smiles knowingly. After searching the house thoroughly, Marybeth and Ray sit in the living room and Marybeth asks why he's so fixated on the Accountant. Ray tells Marybeth that Francis Silverberg used to be the accountant for the Gambino crime family, in addition to other criminal leaders. As Francis was getting older, the Gambinos were afraid that he would might eventually rat them out, so with his life in danger, Francis went into protective custody in prison. In prison, he met Christian and took him under his wing. He taught Christian about his business and his clients, and told him that his mistake was staying in one place for too long. Christian was later moved to a different facility to help the government financially track terrorists.
At some point, Ray was placed on the investigation into the Gambino family and met with Francis in prison, but Ray didn't take him seriously. For some reason, Francis is released from prison where he is no longer protected. The Gambinos catch him and torture him and kill him. When a guard at Christian's new facility lets him know, Christian grabs the guard's coffee thermos and smashes him over the head and escapes. Since Ray didn't take his interview with Francis seriously, he felt partially responsible for his death. Marybeth asks why Christian was in prison in the first place.
Ray tells her that Christian's mother died, and he and his father, who were both in full military dress, went to the funeral where they saw her new husband and their two young boys. The new husband tried to have them escorted out, and Christian responded violently. Christian's father tried to break it up and was shot and killed by accident. Ray asks Marybeth about her background and the charges on her record. She explains that the man she assaulted was a drug dealer she was trying to get her sister away from. She pistol-whipped him and locked him in the trunk of a car, but it was worth it as her sister grew up to have a normal life with a career and family. Ray tells her that later on, he sat in a surveillance truck for months outside the Gambino headquarters with nothing to show for it when one day, a man walks up and kills the two mafia guards standing outside. Ray runs inside rather than waiting for backup, to find multiple dead bodies inside (connecting to the opening scene, and the audio recording).
He hears Little Nicky upstairs begging for his life. Based on what he hears and what he sees, he believes that the killer was out for revenge for something deeply personal. Ray follows quietly and is about to enter the room, when Christian comes up behind with him a gun. Christian questions him, and Ray tells him that he's just a lowly Treasury agent. Christian asks if he's good at his job, which Ray tells him he's not. He says he's lousy at his job, but he has children and begs him not to kill him.
Christian asks if he's a good father. Ray tells him that he know he's bad at his job, but he's a great father and he always did right by his kids. Christian walks away. Ray tells this story to Marybeth and then tells her that he planned to retire right away and give up the job, but on the way out the door, he gets a phone call. He picks it up and it's the Voice, tipping him off to a human trafficking ring. He gets the credit for the case.
He later gets another tip about drugs coming into the country, and he is again credited for the case, raising his profile and success at the agency. Marybeth realizes that all of Ray's successes came from the Voice. Ray then reminds her that he's retiring soon, so someone else needs to take the Voice's calls. At first, Marybeth refuses. Then the phone in Christian's house rings.
She answers it, and the Voice tells her to tell Ray to get his feet off the coffee table. Later, the Assassin is setting up a team of henchmen at the home of Lamar, the CEO of Living Robotics, as he was behind the whole plot and killed his CFO and his sister to cover his tracks. The Assassin questions Lamar about Christian, but Lamar is dismissive and says he's just a freak. He also asks Lamar what the point of all of this was. Lamar claims that his ability to help people far outweighs any crimes he's committed. Christian is able to get on the premises and kill the henchmen one by one, leaving only one man and the Assassin, who has been monitoring the situation on surveillance cameras. As the Assassin watches, he realizes that Christian is muttering nursery rhymes to himself, which the Assassin recognizes. The last remaining henchman has a gun on Christian, but the Assassin bursts in and tells him to stand down.
The henchman ignores him and is about to pull the trigger when the Assassin kills his own henchman. Christian stands up from behind his hiding place and greets the Assassin, "Hello Braxton," revealing that the Assassin is Christian's younger brother. The two men are surprised to see each other as they haven't seen each other in 10 years. As they talk, it becomes increasingly antagonistic. Braxton blames Christian for their father's death because Christian wanted to go to their mother's funeral, even though she abandoned their family.
Christian lets Braxton take his anger out on him without fighting back. Lamar watches all this on the surveillance cameras incredulously. Braxton challenges Christian to fight back, asking him why he (Christian) didn't turn to him for support, and he's always been there for him his whole life. Christian does fight back and they finally end up on the floor, both tired. Lamar enters the room and asks what the hell is going on.
Christian abruptly shoots Lamar, and then offhandedly apologizes to Braxton, saying he had to finish what he started. Christian gets up to leave and Braxton asks if they can meet again soon. Christian tells him that he'll find in about a week. Christian leaves a note for Dana in her hotel room, telling her that she deserves "wow". He packs up his trailer and drives away. At another press conference at the Treasury Department, reporters ask about the scandal surrounding Living Robotics and the recent death of its CEO and how the Treasury Department was able to solve the case.
The director calls up the agent in charge, Marybeth who follows Ray's cue and simply cites good old-fashioned investigative work. Dana is back in her apartment and repairing the damage caused by the fight when she gets a mysterious package delivered to her. She opens it up to find a painting, seemingly expecting the Pollock she saw in Christian's trailer. Instead, it's the painting of dogs playing poker. She laughs, but when she notices the canvas seems to be loose, she pulls at it and realizes the Pollock is underneath the dogs. The final scene takes place at Harbor Neuroscience. Two parents are talking to the same psychologist from the beginning, telling him about their son. Their son wanders through the house.
The psychologist tells the parents that the outside world will treat him like he's different or dumb, and then he will be burdened by the low expectations. Most of the other people in the house are children, but the boy wanders into the room of an adult woman who is screaming and shaking and smacking herself in the head. The boy's parents come in and apologize for their son wandering in. The woman calms down briefly as she looks at the boy and seems to smile at him. The psychologist tells them that the woman's name is Justine, one of their few full-time residents.
She's unable to communicate verbally, but she can do so using her computer. He suggests that the boy hang out with Justine while he finishes giving the parents their tour. They agree and leave their son with Justine who seems to have calmed down. The parents ask the psychologist about Justine, and he explains that she's his daughter and the reason he started his institute.
They also ask how they are funded, and he tells them that they have some very generous benefactors. The father asks if that is how Justine has such an expensive computer. He explains that he's an engineer and that her computer is powerful enough to hack the Pentagon, which the psychologist didn't realize. Back in the room, Justine goes to her computer while the boy looks around the room. He sees a framed puzzle of Muhammed Ali on the wall. Justine sits down at her computer to show the boy how she communicates. She types something and the Voice greets the boy. She smiles and a photo on the wall shows that she is the same young girl at the beginning of the film who connects with young Christian over the puzzle.