The movie starts out with a sea of teenagers chanting the name "Charlie" in a large auditorium. Charlie (Anton Yelchin) buttons up his shirt, ties his black Chuck Taylor high-tops and puts on his blazer and then proceeds on-stage saying, "Thank you, how's everyone doing tonight, It's great to see all of you here, my name is Charlie Bartlett!"(Important later). With each word, the fans cheer louder and stronger. Then after being snapped out of a daydream, we see that he's in the principal's office and that his mother has just arrived.
His mother Marilyn (Hope Davis) asks the principal if Charlie's grades or attendance are an issue and the Principal says that he's an excellent student but a bit unusual. The principal proceeds to tell Marilyn why her son is to be expelled by showing her a fake driver's license. She shows no signs of being displeased so he then dumps an entire box of fake Id's on the desk saying that he's been running a laminating press from inside his dorm room. The principal speaks highly of him, so Marilyn then pulls out her checkbook and asks if he'd like an endowment. However, he says that it is illegal for Charlie to be making the I.D.s and that they can't overlook it.
On the car ride home in their towncar/limo, Marilyn tells Charlie that she's not mad, but just doesn't know why he did it, because money isn't an issue. Charlie says that the other kids were just starting to like him, and Marilyn says that there's more to high school than popularity. In a witty remark Charlie says, "Like what specifically?” and Marliyn says that nothing comes to mind. She says that they'll try public school.
While playing the piano singing the theme song from "All in the Family" with Marilyn, Charlie says that he'll be taking the bus to school tomorrow instead of being driven by the chauffer. He then reminds her to take her medicine and she washes it down with a glass of champagne.
The scene shifts to principal Gardner (Robert Downey Jr.) as he pulls his car into the garage while hitting the antenna on the door. He comes inside to a house of blaring music and opens his daughter Susan's (Kat Dennings) door to reveal a stereo cranked up, Laptop on, TV on, while she's on the phone. He gives her what he calls "crack rock" (rock candy), and wants to at least say hi and talk for a minute but she somewhat rudely shuts the door on him. He then pours himself a bourbon and checks his phone messages, one being from the superintendent saying that he'll be at the school when they make a security camera announcement, and the other being from his ex-wife saying that their daughter won't return her calls. Afterwards, he sits outside in his captain's hat and drives his remote-controlled boat around the pool.
The next day, Charlie stands at the bus stop, with his Blazer, slacks, tie, neatly fashioned hair and briefcase type bag. The bus that pulls up is indeed a short-bus and the bus driver asks if he's on the wrong stop. Charlie climbs aboard passing an array of misfits and nobodys. He sits next to a very large mentally handicapped student who's eating a lollipop, saying that his name is Len (Dylan Taylor). He then pulls a sticky sucker out of his shirt pocket and hands it to Charlie who graciously accepts.
As he makes his way across the campus of Western Summit High School, girls laugh at him, people comment on his tie, and people are walking around smoking Marijuana. At his locker, Susan asks why he didn't get a locker in the teachers lounge because he looks like a teacher. She then announces try-outs for Henry IV and Charlie signs up, which grabs her attention. As he goes into the bathroom to wash his hands, Murphy Bivens (Tyler Hilton) stops him asking if he has a briefcase, and Charlie replies with sarcastic wit with questions about the patch on his blazer and asking about rhetorical questions making Murphy look like a complete moron. Murphy then shoves Charlie’s head into the toilet and is immediately interrupted by Principal Gardner who just sends Murphy and his friend to class.
At lunch, Charlie sits next to some "popular" looking kids and introduces himself only to be rejected as they walk away. Len the comes up to him and Charlie asks him to sit with him, which catches Susan’s eye once more as she smiles.
At the play auditions, Charlie does a monologue about a girl's first period and Susan enjoys it with a hefty smile while the other judge sends him on his way. Immediately afterwards outside, Murphy kick Charlie's A$$ as Murphy's friend videotapes it.
At home, Marilyn asks if he made any friends only to have Charlie show her his black eye. She tells him he's not going to school the next day, but seeing a therapist instead. At the therapist’s office, he says that he doesn't fit in because he's abnormal and backs it up by saying, " My family has a therapist on call, how normal can I be?” Charlie then proceeds to tell him about his fantasy which was at the beginning of the movie. The therapist asks about how he feels about his father leaving and Charlie quickly dismisses it by saying that he also worries about gas prices in class, then his therapist prescribes Ritalin.
Charlie then takes the patch off his blazer, and is welcomed back at school by Susan and shoved by Murphy. In class he passes a note to Susan introducing himself and she just responds by saying "I Know". At an assembly, It is announced that Security Cameras will be installed in the student lounge, and after a brief outrage by students, Charlie goes out and pulls the fire alarm, which Susan notices and somewhat admires.
On his first day of Ritalin at home, Charlie is doing vast amounts of homework at the dinner table, which his mother doesn't particularly approve of. Then he seems to spaz out even more, by playing the piano franticly, and running laps inside an empty pool. The eccentric behavior just seems to escalate over the next few days. On the 4th night, he runs outside pounding his chest in his underwear speaking gibberish, telling everyone in the neighborhood to wake up. He's then brought home by the cops. Charlie is playing the piano in the blazer and sunglasses as he narrates the conversation between Marilyn and the cop, as they discuss his new medication.
On the bus the next morning Charlie asks Len if he'd like to make $50 after school. We then immediately see after school, as Murphy is walking the train tracks home as Charlie’s limo pulls up next the him, and Len pulls Murphy into the car, restraining him until he settles down. Charlie then gives a list of reason on why Murphy is such an angry person, such as: he was picked on as a child, Dad's an alcoholic, Cheerleaders laugh at him, and teachers make him feel stupid. Charlie then says that he wants to be Murphy's friend, and Murphy says that they're too different for that to happen. He then says that they could be business partners by selling 90 pills of Ritalin at $10 a piece, and Murphy accepts.
At home, Susan asks her dad for a 1 a.m. curfew, and leaves for the dance. At the dance, Murphy tells Charlie that he's sold all the pills, then two topless girls run out of the gym followed by Len wearing a bra and cape. We then see that everyone inside the dance is high on Ritalin.
The next day, at school, Charlie is welcomed in the halls by cheers and praises. Meanwhile, outside the security cameras are being installed in the Student Lounge.
Charlie is the confronted by a shy, nervous boy named Kip (Mark Rendall) and asks for a minute of Charlie's time. In the bathroom, Kip asks Charlie if he can get ahold of some depression medication and gives him a list of his symptoms, and Charlie’s agrees to help him. After doing research on the subject, Charlie go to his therapist and gives him the list of symptoms claiming them as him own troubles, and is prescribed to Xanax and Zoloft.
At school he has a type of therapy in the bathroom where he sits in one stall and Kip sits in another. He gives Kip his diagnosis and tells him to take the pills as needed, as Murphy bottles up the medication.
At the dinner table, Charlie’s mom says that his medical problems may be because of her and that he's working on making friends.
Back at school, a Pharmacy sign replaces the restroom sign as he has various students come in and tell him their problems such as parental, boy, drug, school, and breast problems.
To get medication, he routinely goes to therapists claiming he has the symptoms of his patients.
At school, He's welcomed by even more praise, and the line of students waiting outside of his “office” gets even longer. The principal heads towards the bathroom as the doorman tells him to get out, which they do in the nick of time.
Once again at the therapists office, the therapist tells him he's glad he's responding well to the medication, in which he replies, "Introducing teenagers to medication is like opening a lemonade stand in the desert".
At Murphy's garage type hangout, as they count their money, Charlie and Murphy are watching the video of Charlie getting beat-up by Murphy, and says that they should make it up to the kids he's beat-up. They decide to make a movie dubbed "Greatest after school fights”, which is just Murphy beating up 5 or 6 kids at school. They sell the DVD in the student lounge and giving they kids who were pummeled, $20. Charlie is then called into the principal's office and suspended for 3 days for selling the video, although he tells him he doesn’t understand what he did wrong.
Charlie spots Susan walking down the street and asks her to hang out with him and as she gets into the car, the police officer that was at Bartlett's house earlier watches. At Charlie’s mansion he plays the piano and sings with Susan, and just before a kiss, Marilyn who prances in singing and is introduced to Susan interrupts them. She then asks about his dad, and he makes up a long story about him being hit by an ice cream truck. He then blows it off and resumes piano in a humorous version of Yankee Doodle.
At a bar, Principal Gardner is sitting, drinking a bourbon, when the police officer we've seen a few times, tells him that Susan has been hanging out with Charlie Bartlett.
Now at the Gardner home, Principal Gardner tells Susan to shut off the power grid of a room and interrogates her about Charlie, stating that he only wants her so he can say he slept with the principal's daughter. He then proceeds to drink more and plays with his boat, which he crashes off walls.
The next day, Marilyn tells Charlie to get up and they're going to visit his dad who is in prison. While there, Charlie stays in the car while his mom goes in, and when she comes out tells Charlie that his dad loves him.
At his first day back to school, he meets with Principal Gardner who asks him if there isn't a private school he hasn't been kicked out of and then tells him he knows that he's seeing Susan. Although he says he's not going to intimidate him, he does in a subtle manner. In Charlie's "office" Susan sits and asks how his little therapy sessions work and although Murphy is bound by a confidentiality agreement is asked to leave the room. They talk about her dad, and Charlie says nothing about his intimidating talk. Charlie asks her what she thinks about her dad, and she goes off about the night her dad found out about her mom's affair and that he got drunk waving a revolver around and how his mom left but then she stayed with him and that's where his hobby with the toy boat and drinking came from. Charlie simply replies by saying," Susan, I'm still waiting for you to tell me how you feel about your dad". She just says that it's hard to have one parent ditch and the other lose their mind, questioning how she can turn out even remotely functional which he briefly reflects on. She says the little session make her feel somewhat better as he walks up for the first kiss.
Now back out at the student lounge, Murphy throws his leather jacket over the security camera, as Principal Gardner notices, and announces that Charlie is throwing a party at a Drive-In themed club, which is a guaranteed raging party.
While at the party, the band rocks out, and Charlie is called upon by the captain of the football team for advice. He tells Charlie that he wants to go to Paris and study painting which Charlie encourages. He tells him that kids are supposed to P!$$ of their parent occasionally. After hearing that, Charlie tells Murphy that he seems jealous, and Murphy tells him that "IF" he is, it's because he gets hot girls like Whitney Lauderback (Cheerleading Captain). He then says that he would want to treat her right with dinner and a movie and Charlie tells him that he'd have to clean up which Murphy refuses. Then asked why he quit doing the school play, Murphy says that he kept on getting his A$$ kick by people like himself.
Susan then comes up to Charlie stating that he needs to step into her office, which is on a balcony inside of an old painted up car behind a curtain. They cuddle up together and she asks him a couple of questions, and if he answers truthfully he will receive a reward. First, is he only interested in her because her dad is the principal? After he truthfully doubts it, she gives him a kiss. Second, she asks him what the deal with his father is, and after a moment of discomfort, Charlie says that he's in prison and that he had to take care of his mom since then. Susan just replies with, "So who's been taking care of you?” And as they start kissing, he says that he's never done it before, which she says "I know that Charlie Bartlett". So they end up having sex while the party is going on, and afterwards, she smokes a cigarette and he jumps out of the car in his boxers saying he'll be right back. He throws on his blazer and stands on the balcony living his fantasy by saying, " Ladies and gentleman how're you all doing' tonight? My name is Charlie Bartlett and I'm no longer a virgin". The crowd cheers for him and Susan laughs in disbelief.
At home, kip is Writing a suicide letter on his computer and he then takes about 10 of the pills that Charlie had given him.
The next morning, Principal Gardner arrives at Charlie’s house, and he sits Charlie and his mom down, telling Charlie that Kip had overdosed the previous night, that he's ok, and that Charlie is just lucky he didn't tell his parents where he'd gotten the drugs. Principal Gardner says that if he could explain what he was doing and why it may be a different situation. Charlie says that he's helping the students and that nobody else will listen to them, but is told that it's ok the listen but he's not a doctor. After a small rant about how drugs can help people and that some people feel it's better to be "zonked out of your mind" than to deal with your problems. Charlie asks if he's speaking from experience and he willfully says that he sought "treatment for some issues". Charlie asks if he'd like to talk about it sometime, but is put back down and asked why he's doing it. Charlie says that for the first time, everyone likes him, and that he's happy where he is. Principal Gardner tells him that there are more important things than popularity and Charlie rebuts by saying, "I'm 17 and popularity is pretty damn important to me". He's then told that popularity isn't the most important thing, but it's what he does with the popularity.
Later on that day, Charlie goes to visit Kip, who says he got his stomach pumped and that he gets to sit around and play video games all day. He appreciates that Charlie came by but says that he still has problems and that there's nothing that can be said to make him feel any better. Charlie tells him that the universe is huge and out of all of the single celled organisms on other planets he was born here, in the time where were have awesome music, technology, food from all over the world, and internet porn, and that the odds of that are astronomical, and for that he has everything to live for. After that doesn't work, Kip asks Charlie to play "KillZone" which cheers up Kip a bit. Kip asks if Charlie is selling drugs anymore and he says no, and Charlie asks him if he has any new ideas on stuff to do, and Kip says that he's been writing a play but no one will read it.
We then see Principal Gardner shut down the play mainly because of its title, "Hell comes with your own locker". He says that it's too inappropriate, and Kip and Charlie argue that it has truth to it and it's how kids really are. Kip then says, "If it helps your decision, I'd be considerably less likely to end my life if you said yes", and Gardner just tells him that they need to get it through drama club. Charlie says that he's got Drama Club taken care of.
In the bathroom Murphy is trying to talk Charlie out of flushing all of their pills, and after he complies, he still tries to conceal more pills which Charlie’s flushes.
Down at the student lounge, Charlie stands on top of a pool table and announces that he will no longer providing medication, and that many people are done speaking to him which he doesn't mind, but he will still be holding his bathroom sessions as usual. Murphy then sarcastically says, "I'm one of those people not speaking to you".
As he makes his way up to his office, the line in front of his door is longer than ever. Whitney Lauderback is Charlie’s first patient, and she reveal that she's slept with most of the football team, and that she doesn't like saying "no". That she wants a guy to take her out to dinner and a movie, and Charlie says that there's a guy out there that would be willing to do that.
Next we see Murphy dressed in a popped collar blue polo shirt with his Mohawk fixed to look presentable and a nice looking orange convertible outside Whitney's house. He gives her flowers and they both say that they'd never been on a real date before.
Charlie is then informed at school that the petition to ban cameras has been disregarded and that a protest will be held out in the student lounge. So the next morning there is one student outside the lounge stating, "This is a school, not a prison" with a megaphone and sign. As the day continues, more and more students join the protest. Charlie’s agrees with the cause of the protest but also sides with Gardner on a few points. To avoid getting everyone at the protest getting suspended for 3 days, Charlie tells everyone to come back later that night.
After school, Charlie walks up Susan's driveway with a pharmacy bag and Susan greets him with a kiss, which Gardner watches, and spazzes out when he sees him give her the bag. He runs outside demanding to see what's in the bag and Susan declines. She then tells him not to make her choose between him and Charlie as the argument escalates, and includes saying that Charlie has done more for the school than he ever will. As she walks away, Gardner grabs Susan's arm, Charlie grabs his, and Gardner pushes Charlie, which leads Charlie to punch and knock down a drunk Gardner. Susan throws the bag at her dad, and he opens it to reveal a box of nicotine gum.
At the protest that night, Charlie does his fantasy speech and tells the students, " If there's one thing I want you to walk away with tonight, It's that you guys don't need me, I mean it, you think I'm any less screwed up than you are? I get up every morning and I look in the mirror and I try and figure out just where I fit in, and I draw a complete blank. You guys are looking for me to try and tell you what to do? You need to stop listening to me, Stop listening to people telling you who you should be, and stop listening to people telling you that your not good enough to do the things you want to do". He's cut short by cops who make their way through the crowd and they arrest him for assaulting Gardner. As he's loaded into the back of the car, the crowd chants his name as Gardner tells them that because of Charlie, the student Lounge is now a detention center. They react by smashing all of the cameras and completely trashing the lounge. As the superintendent watch the mayhem, he tells Gardner that he's fired. The police reappear and the mob scrambles away.
The next day in jail, the reoccurring police officer tells Charlie that his mom came to bail him out. His mom says that she doesn't know how to feel about what happened and Charlie tells her that she should be mad because he just got arrested and a bunch of his friends just trashed a building. She says that it might be her fault because she always treated him like an adult instead of a little boy. He says that he wouldn't know what to do with him either, and Marilyn tells him that he's grounded. When she asks what the normal amount is and he says 24 hours and she says that since he acquired a misdemeanor they'd better make it 30.
After Gardner hears Susan sing she scowls at him, he goes back to drinking his bourbon.
Soon after, at the opening of the play, Charlie asks Susan how her dad is doing and she says that he's locked himself in his study and that he probably doesn't want to be around a group of people who hate him.
So Charlie goes to Susan's house to talk to Gardner and after no answer at the door he lets himself in and looks around the house seeing it a wreck, He finds him outside with a bottle of bourbon in one hand and a revolver in the other. He scares Charlie into sitting down after firing a shot into the pool. He shoots his toy boat and continues to fire shots into the air, saying how much he's displeased with him and how he's turned everyone against him and taken everything away from him. Charlie says he wants to help but he can't because he's just a kid. This slightly pleases Gardner as he turns around with the gun and raises it to the air near his head. Charlie tries to stop him but falls off the deck, cracking his head off of the diving board and floating to the bottom of the pool. Gardner dives after him and pulls him up into the shallow end. Asking, " What the Hell did you do that for?" Charlie says, " You were going to kill yourself", and Gardner just says, " Can't kill myself, got too many responsibilities". He then tells Charlie to never ever attack a drunken guy with a gun. They get Charlie some dry clothes and clean him up to go to the play. While Charlie is changing, Gardner tells him that there are worse things than a parent in prison for tax evasion.
The play is a stage cut in half with parents commenting on their children’s actions, and on the other side Susan being peer-pressured by a boy. We then see that the peer-pressure is over singing. Susan Sings and notices her dad and they exchange smiles.
We then see clips of Charlie and his Mom going and visiting his dad in prison and of Gardner back to teaching history. Then Charlie is at a Psychiatric Institute interviewing for a summer internship. As Charlie is being interviewed the interviewer tells him he has a hell of a day in front of him. In a witty fashion, Charlie asks, "Would you like to talk about it?”
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