Montgomery Adams, Monty, is a young boy who is going to be staying with his uncle, a scientist who lives in Pittsburgh, while his mother is away for a few months in South-east Asia. He does not seem to mind though, because he understands why his mother could not take him with her. Due to a lack of proper schooling in the jungles of Borneo. Luckily, his cousin Nan will also be there, who he happens to get along with very well, considering they are also the same age.
However, despite his lucky life, Montgomery goes on about how he hates his name and also cannot stand his red hair. Uncle Leo spends most of his time in the basement laboratory but he does take time from his busy schedule to greet Monty. Especially to prick him with a pin, then offer him a doughnut that was fried in peanut oil, and Monty happens to be very allergic to peanuts, which results in him throwing up. Uncle Leo suggests that Monty drinks some a jug of cider to remedy this.
Monty has to transfer to the new school mid-semester, but luckily he knows a few of Nan's friends already, and also happens to have a crush on one of them, Ashley. Strangely, his teacher gets miffed when Monty asks which desk is his, then she claims she already told him last week. But Monty was just in another state, until a few days ago. He was not there last week but Ashley helpfully points out the location of his desk for him.
After school, Monty kills time around the mansion while his cousin takes a piano lesson. It turns out both he and Nan are really good at piano playing and they decide they can perform a duet for an upcoming event. While waiting for his cousin to wrap up, Monty opens the door to Uncle Leo's Forbidden Basement Laboratory, where someone with a high-pitched voice yells out for him to get out. Uncle Leo surfaces a few moments later and apologizes for snapping, but his basement laboratory is just too dangerous for non-scientists.
At school the next day, Monty and Ashley are in art class making casual conversation with one-another. Including minor flirting and goofing off. Monty accidentally then spills paint all over a rough classmates' volcano. Leading the both of them to be punished and given after-school detention. Ashley then snubs Monty, rather upset with him but she does confront him at the end of the school day where she explains she caught him messing up the art room, then sneaking out the window.
Monty goes to examine the damage, but then asks why Ashley thinks he did it and he even points out he was in Science class at the time. But Ashley insists she saw him do it, then she goes to tattle on him to the principal.
While cleaning up the art room by himself, Monty suddenly spies his reflection in the mirror... only to realize the reflection is of someone behind him. Monty tries to chase after the figure but he's stopped by the art teacher who chastises him some more and explains how mirrors work.
After school, things aren't much better as he gets beat up by guy whose volcano he accidentally ruined. The following day, Monty spies his double again, this time looking through the classroom window. Monty runs across the room and jumps out the window to chase after his double, only for him to get into more trouble.
Once at home, Monty greets his uncle, then asks if he has a twin. Uncle Leo admits that he does, quietly explaining that his mother was pregnant with two children, but his father died a month before she was to give birth. Due to this, she could not afford to raise two children on her own so she had to give one up. She chose to keep Monty, due to him being born first. Monty has a lot of questions, but before he can ask about the twin tormenting him at school, Uncle Leo drops a shocker: Nan is his fraternal twin. Uncle Leo raised her as if she was his own daughter.
Nan and her brother then begin to discuss her true feelings, involving the abandonment and how to deal with this new information about their relationship. They also share a story about one Christmas when they both stole part of one of their cousins model trains and they should have known they were twins then. But before they can continue, they are interrupted by a telephone call who warns Monty that things are going to get a lot worse...
Several weeks pass though before anything gets worse though, so Monty does not believe this mysterious caller. However, on the day of the Big Piano Rehearsal in front of the school and things unfortunately do get worse.
Before Monty can go onstage with Nan for their duet, he realizes he left his sheet music in his locker. Along the way, someone shoves him into a supply closet. He escapes the rising fumes of some carefully spilled chemicals and races to the auditorium, only to discover when he returns backstage that Nan went out and started without him. Only to see that she is with him. Only, the him on stage is not really him. The real Monty yells out to the Fake Monty, who cuts the recital short by pushing the piano across the stage in an attempt to kill the real Monty. Who then gives chase to the twin but he is suddenly confronted by the twin who informs him that he plans to take over his life and he punches the real Monty in the stomach before leaving.
The Real Monty gives chase and sees the Fake Monty calmly walking past cars in the parking lot and along the street holding a spray can. He stops to spray-paint a heart around "MONTY LUVES ASHLEY 4EVER" on the door to a car he knows Ashley will pass on her way home and Monty continues to follow him home. He spies the twin slip into one of the mansions open windows and Monty races inside to get his uncle. But then remembers he is not home.
Nan however shows up and angrily asks why he shoved a piano offstage but Monty is not able to give a good answer and they argue until coming by a computer to discover a scholarly paper authored by their uncle resting in the printer that explains everything.
Monty picks up on the subtle clues and realizes his uncle must have cloned him, with the pinprick earlier in the book an excuse to get a blood sample. Nan insists he would never have done such a terrible thing but Uncle Leo exhibits some excellent timing by interrupting her to confirm that he indeed would do such a terrible thing. He claims however that he is a Scientist, so he had a perfectly good reason for doing it. Uncle Leo summons four cloned Monties, who line up behind him and they then attack.
The children panic and begin throwing glass beakers at them in a futile attempt to escape. Uncle Leo cries out for them to stop breaking all his expensive equipment. The escape is thwarted when the real Monty accidentally knocks himself out soon after when his head collides with a steel table. He soon awakens in a supply closet and spies Nan and... the real Uncle Leo?! He then explains that the other Uncle Leo is his own clone, but by the time he realized that the clones were evil, it was too late and he was overcome by his clone. He also reveals that he actually cloned Monty a year or so ago, the pin prick thing was just a coincidence. Uncle Leo did not know about the Monty clones until a few days prior, and it turns out they had been sleeping in some of the extra bedrooms in the mansion. When he tried to confront Leo Two about the squatters, he got locked in a supply closet.
Then Uncle Leo shows what a scientist brings to the table by revealing that all the clones have a small blue dot on their right thumb, so that they're easily identifiable against the original. It is then the Leo clone comes in to drag the real Monty out of the supply closet and he forces the Monty clones to hold down Monty so that he could tattoo a little blue dot on Monty's thumb. Thankfully, before the Leo clone can also tattoo Nan, Monty manages to make a diversion so that she can escape and get help.
The four Monty clones then decide to hold his hand over a bunsen burner to show that unlike him, they cannot feel any pain. Monty tries to sleep through the pain of his badly blistered hand but he has difficulty and tries a meek escape. Besides being evil, and cannot be harmed, they also are light sleepers. They easily thwart any means of escape when suddenly the door is kicked in.
It's Nan and she has brought scientist to the rescue! The clone Leo is angered by the strangers but he falls into their trap, as the scientists Nan brought were old college roommates of Uncle Leo. They then force the clone Uncle Leo into the waiting truck outside. The Monty clones also do not bother to aid the Uncle Leo clone. The scientist then also locate the real Uncle Leo in the closet before explaining that they will be taking all of the clones down to South America. Where they have set up a lab to do testing on the duplicates. The real Monty tries to embrace Nan in gratitude, but she shuns him due to his tattoo. Things are not helped much by the other clones all claiming they are the real Monty too but Nan thinks she knows which one is the real Monty when he recites the Christmas anecdote about the trains. The real Monty is then shipped away with the rest of the clones.
The Real Monty realizes that his clones do not realize he is not one of them, they think the clone who stepped forward was indeed the real Monty. Soon the truck arrives at a loading dock, the clones discuss how they are probably being held until morning when they can be loaded onto a ship bound for South America as Monty spies an armed guard standing watch outside the back door to the trucks compartment. He also finds an emergency hatch on the roof of the truck and manages to get all of the clones to work with him by turning against "himself". He inspires the clones to work as one and escape, so that they can reclaim "their" life from the original who is living it.
The Monties begin standing on each others shoulders, with the real Monty planning to climb out the top. He tells them he'll come back with a rope to get them and they believe him. He manages to get out, but accidentally hurts his burned hand! After crying out in pain, the clones yank him back inside. They then plan to kill him but he makes a final request to pick another name, considering he has always despised his own. He proposes Paul. One of the other clones likes Paul and decides he might like to be called Paul too. Another clone comes up with his own name he would like to be called. Before long there is a brawl among the clones over who gets to be named what.
While his copies are distracted, Monty alerts the guard to the fracas and slips out unnoticed while the guard goes inside to break it up. Monty walks all night until he finally arrives at the mansion. The book then switches into Nan's own perspective. She is confronted by both Monties, claiming to be the real one and she decides she will test them by giving them half one of the donuts fried with peanut oil. Leo warns her that they don't know how allergies work with clones, and it is possible the clone will also has this allergy.
But they go on with the experiment and both Monty's are given a doughnut. Monty then proceeds to vomit...
It's revealed that the Monty who threw up was a clone! He practiced vomiting the day before so that he could prepare for such a test. Should it ever come up. He also only knew this story because he overheard Nan and Monty discussing it earlier.
Clone Monty shows no remorse for sending the original to his doom, then proceeds to utter the books titular line, "I am your evil twin!"