Artist Wendy Watson is working as a temp secretary at A.N.D. Laboratories, answering the phone and playing with her father's Zippo. In her spare moments she tries to assure her mother she has an impressive job. She's unaware that the experiment in the laboratory behind her has gone wrong until a composite DNA monster made up of dozens of limbs and tentacles breaks free. She drops her lighter and stabs it with a letter opener but is driven back when a smug-looking man arrives to shoot the creature. He ends up using a taser on it, causing it to blow up. He tells Wendy to keep the secret or die, and she agrees to keep the secret. He confirms she's telling the truth using a wrist device and compliments her, saying she's good under pressure. He notes he's just The Middleman, and slips away as the fire-fighters arrive.
At an Italian restaurant, Don Colfair tries to determine who killed the Spoldoni family from a witness. He's interrupted when a shadowy figure in a trench coat bursts in and guns down everyone except the witness, who slips out. The killer departs, leaving nothing but a banana.
Wendy meets with her temp supervisor and learns that the police think her lighter caused the explosion. Wendy explains that the lighter belonged to her father, who died in an airplane crash, and she didn't start the fighter. She considers telling the truth but realizes The Middleman would kill her if she did. She tries finding a job without success and then goes back to her illegal sublet that she shares with another artist, Lacey Thornfeld. Going in, she chats with neighbor Noser, who plays the guitar in the hallway. Lacey explains that her animal support group will be leading a protest at a French restaurant that cooks rabbit. Wendy has taken a message from Wendy's boyfriend Ben to meet later, and a call from a temp agency that Wendy has never heard of.
Wendy goes to the Jolly Fats Wehawkin Employee Agency and is greeted by the supervisor, Ida. Ida puts Wendy through a series of grueling tests and finally just stares at her for a moment then introduces Wendy to her new boss: The Middleman. He explains the temp agency is a recruitment center that he uses to hire agents for… special problems. He's a contractor who deals with exotic situations involving mad scientists, androids, and monsters. He has Ida demonstrate she's actually an android but Wendy is unimpressed, and The Middleman notes that she has a high threshold for the unexpected and the unknown. The Middleman notes that she is a skilled video gamer but schedules her for an appointment with Sensei Ping for martial arts training. Wendy only wants to paint and The Middleman notes that he gave the cops the Zippo to frame her so she'd have to come to him. Ida mentions a new job he has at an Italian restaurant and a furious Wendy storms off.
Back at her sublet, Wendy has a brief exchange of trivia with Noser and finds that Ben the film student and boyfriend is in her bedroom. She meets him and tries to embrace, but Ben withdraws. It turns out he has a video camera and his friend Eddie, and his professor thinks he needs more pain in his life. So he breaks up with Wendy on-camera and she provides some more pain by attacking him and driving him out. She sits down to paint and works on an image of the DNA monster from the laboratory.
The Middleman goes to the Italian restaurant with fake FBI ID. He starts to scan the place but is interrupted when Wendy arrives. He figures that she remembered the address from the agency and she admits that she has no choice but to take the job given her current employment situation. He explains that he works for someone, but he doesn't know who, and weapons and equipment just come in. He then finds the banana that the killer dropped and concludes an advanced intelligence is behind the murders. Wendy accepts the job.
In an alleyway, another mob catches up to the witness from the restaurant and demand he identify the killer. He starts to do so but they're interrupted when a banana falls from the fire escape above. The killer is there, and guns them down.
Ida is doubling as an electron microscope and examining the banana, and finds genetically engineered spittle. They head out (leading Ida still plugged in), and go to Simionics Animal Laboratories impersonating sanitation inspectors. They meet with Dr. Gibbs, the head of the project to genetically engineer intelligent gorillas. They notice a cage with police tape and Gibbs explains that Spanky used to live there. Wendy notices some discolored paint and finds a secret room filled with Mafia memorabilia and bananas. Gibbs didn't know about the room but can't figure out why since Spanky's mind is controlled by their mainframe, along with the other gorillas. She explains that Spanky was died in a flight simulator accident, but as they leave, The Middleman figures that Spanky faked his death and they can't let a super-intelligent ape gain control of the Mafia.
They go to the Andolini Social Club, where the wise guys hang out. The Middleman plans to order a glass of milk and then get the information he needs. Wendy refuses to go and he has her hold his equipment. All of his equipment. He goes inside and the wise guys start running. The Middleman emerges with Tino, who runs all the rackets and is in good with the new boss. The Middleman enjoys some milk while slamming Tino's head into the car and explaining that he was a Navy SEAL and was taught over 456 ways of causing pain. He was recruited after saving his squadron and getting revenge on the man responsible. Tino finally breaks and directs them to a strip club where his boss is hanging out.
The duo go to the strip club and confront Snappy, who is negotiating new deals and using a voice synthe. Spanky goes for his gun but The Middleman disarms him. The gorilla makes a break for it and rips off his clothing and voice synthe, then goes over a fence and into the gorilla den in the neighborhood zoo.
The Middleman drops Wendy off at her sublet and she goes in. While chatting with Noser, she spots a banana and a shadow underneath the door. Setting off her wrist alarm and grabbing Noser's guitar, she jumps inside and clubs… Ben, who came back to apologize. He tries to get her to take him back but they're interrupted when The Middleman bursts in to rescue Wendy. When Lacey starts to hit on The Middleman, Wendy gets him outside only for Spanky to open fire. The Middleman goes out to deal with Spanky. When Wendy comes out, Spanky is locked up but he has a new voice box. They figure he got it from the lab and plan to head back. The Middleman insists that on going alone but Wendy insists on going with him. They rappel into the laboratory to access the computer, but another gorilla cuts Wendy's line and she drops to the ground. A gorilla takes her hostage and Dr. Gibbs emerges to say she's behind the whole thing. The Middleman is forced to relinquish his gun and Gibbs explains she went into the mob business to raise money to take over the world with super apes. The Middleman threatens to blow up the computer but Gibbs calls his bluff and orders her gorilla to open fire. He drops to the ground as the gorilla's gunfire hits the computer, destroying it. He sets up Gibbs to be taken in by the FBI but Wendy has an idea for what to do with the innocent brainwashed gorillas.
Later, Lacey and her activists get the gorillas released into the wilderness and publicize their anti-rabbit killing campaign. The Middleman praises Wendy for her efforts, although she's unhappy that she was used as a hostage. The Middleman notes that maybe next time she'll listen… and then gives her back her father's Zippo. She goes inside and starts painting her newest adventure, while describing to her mother how happy she is with her new job.