Nick Powell (Justin Chatwin) is a "perfect" high school student leading a "perfect" life. Teen angst plays a big part in his psyche. Annie Newton (Margarita Levieva) is a broken teen who acts out her hatred on everyone, especially Nick. When Nick is beaten within an inch of his life, it becomes the job of his spirit to save himself by finding his body before it dies. But how is going to do this when he is The Invisible?
Mom (Marcia Gay Harden) is making a toast to her high-school age son, Nick, at a large gathering. She gives him an inscribed gift. "To Nick, from Mom, make me proud." Following this, Nick proceeds to go the food table and cut the center out of a chocolate cake, taking his piece with him in his bare hands as he heads to the garage. The next morning he awakes in a start. Mom has made him two eggs and bacon arranged on a plate in a happy face. Mom is bugging him about college prep but Nick wants to take a writer's course in London.
At school Nick delivers a French essay to fellow student Pete Egan (Chris Marquette). Pete is attacked in the bathroom a group of kids led by Annie for "accepting merchandise and not paying for it." Back in class Nicholas presents his oral poem. The class is engaged as he recites, interrupted by the ringing of the class bell. Nick catches up with Annie group and pays for the merchandise whispering to her "you are so broken." She attacks him in the cafeteria and they both end disciplined. Annie goes home to her family's apartment. Mom and Dad (Desiree Zurowski and Mark Houghton) fight and she makes sure her very young brother Victor Newton (Alex Ferris) gets fed.
Nick meets up with Pete showing him his secretly purchased plane ticket to London. He complains that mom has has his life mapped out since his dad died when he was 13. Annie goes out with boyfriend Marcus Bohem (Alex O'Loughlin) and he breaks into a car. She approaches a nearby window jewelry display and smashes out the window to steal a beautiful necklace. They take off in the car and evade arrest. She and Marcus argue and she walks out. He calls the police and reports that she's been stealing at school.
The next day at school Pete is watching Annie at her locker. The police arrive and break open her locker. Annie calls boyfriend and tells him he got busted. He plays innocent and she says she knows who did it and will take care of it. Nick says his goodbyes to his friend. Nick arrives home to have his mom tell him the airline called about his flight being changed.
Annie and her gang attack Pete. Under physical torture he turns the gang toward Nick who is at home hosting a party. He meets a girl, offering to let her go to London on the flight that leaves in 2 hours. They start making out and she notices he's wearing an old watch when he has a new one. She learns his father gave him the watch he wears. He leaves the house and takes a walk finding himself being followed by a beat up old car. Annie makes his friend sit in the car while her gang beats Nick senseless. His friend begs them to stop. Nick makes a side comment to Annie and she kicks him into the water. The group checks to find he isn't breathing. They panic. Annie demand that they pick him up and they carry him through the woods, his watch dropping along the way. hey drop his body into a storm drain, cover it and and leave him.
Arriving at boyfriend Marcus' place she confesses to him that she killed him. She needs an alibi. He tries to toss her out citing his probation status. She notes all the stolen vehicles in his shop, dragging her bloodied hand across them. She burns her clothing by the river. In the next shot Nick walks out of the woods to the road in perfect condition. He realizes no one can see or hear him. The police are investigating his missing person status.
Detective Kate Tunney (Michelle Harrison) tells Detective Brian Larson (Callum Keith Rennie) that Nick had a run in with Annie. He notices debris around the entry to the woods. He has a history with Annie's family. A search party is organized. In his bedroom, Nick's mother reads his poetry journal while a bird sits on the porch railing. The bird becomes injured and is dying. A live bird appears on Nick's shoulder and he takes it in his hand. As the bird on the railing slowly dies the bird in his hand disappears and Nick realizes he must still be alive. He tries to lead the search team and he pleads with Annie, who can't hear him, to help. Pete is on the verge of telling the truth.
Det. Larson visits Marcus' garage. He asks about the jewelry store smash 'n grab and he says he wasn't with her. Larson tells him he knows she phoned Marcus. Larson asks about the missing person investigation. Marcus stops Pete outside at gunpoint informing him he's being followed by the police. They go out to the woods where they left Nick. Marcus gets Annie's gang together and they call her saying someone is going tell to confess. She calls Pete to meet her sending him to her gang. Marcus shows up with Annie at gunpoint and sends Pete home. Annie takes the gun when they realize the cops have followed them. She escapes. Nick shouts out to her and she responds, "Never!" Nick continues to follow Annie as she shuns him, he knows his only hope for survival is her.
After sleeping a night in a school gym, Annie goes to Nick's house. She sees his life of his own room and goes through his possessions. She pours ashes from a small bottle into her hand as Nick's mom enters the room. Annie runs out into the wood and goes to the place she left Nick only to discover he's not there anymore. A nicotine gum pack was left leading Annie to see Pete about where they moved him. Pete admits Nick didn't turn in Annie, nor did he. She finds Marcus and takes him at gunpoint to a ledge. Annie and Marcus end up shooting each other but she calls Det. Larson and tells him she knows where Nick can be found. Pete attempts suicide and as he slowly dies Nick finds Pete's spirit standing beside him. Pete's father comes in before he dies, saving him before it's too late.
Nick is rescued from the river and taken to the hospital. Annie fights to get to him despite the gunshot to her abdomen. Nick guides her through the halls to him and he speaks to his mother through Annie. In Nick's room she speaks to him as his spirit moves back to his own body. At that moment, she passes out.
A young boy flies and remote controlled airplane over a lake. Nick notices the boy and is concerned that the boy is alone. He explains that his sister was supposed to come with him but she died. Nick suggests they send her a message. They write, "Hey Annie" on the plane's wings and send it out to fly.