The book begins with the Baudelaire orphans and Mr. Poe on the grounds outside of the school, Prufrock Preparatory School (Prufrock Prep for short). Violet, Klaus and Sunny Baudelaire meet Carmelita Spats, a rude girl who calls the Baudelaire orphans “cakesniffers”. Mr. Poe tells the children to go to Vice Principal Nero’s office. On their way there, they notice the schools’ motto: Memento Mori (Remember You Will Die) which Klaus, being well read, understands.
They soon meet Vice Principal Nero. He explains the rules of Prufrock Prep and tells them that his advanced computer system will keep their enemy, Count Olaf, away. He also tells them about the fine dormitories they have, but that unless students have parental permission, they must sleep on hay in a tin shack (known as the Orphan’s Shack). He considers himself to be a genius and thinks that he plays the violin well, but in fact he is unworthy, stupid, mean, arrogant, obnoxious, annoying and cannot play the violin well at all. Nonetheless, students must attend his lengthy violin recitals every day, or else they must buy him a large bag of candy and watch him eat it.
Reluctantly, The Baudelaire orphans go to the shack and find that it is crawling with crabs, dripping fungus and has horrible wallpaper (green with pink hearts). The orphans then go to lunch, where two women with metal masks serve them their food. Carmelita Spats mocks them again as they try to sit down. They are rescued by Duncan and Isadora Quagmire. The Quagmires tell about themselves. They are in a similar situation to that of the Baudelaire orphans. They are triplets, but their brother, Quigley Quagmire, died in a fire along with their parents. They, like the Baudelaire orphans, were left an enormous fortune (in the form of sapphires). Duncan would like to be a journalist, and Isadora is a competent poet (particularly in the form of couplets). They both have notebooks, or commonplace books, which they use often to write down observations and notions. They become good friends with the Baudelaire orphans.
Violet’s teacher, Mr. Remora, is a man who tells very short, dull stories while eating lots of bananas, and the children take notes. Klaus’s teacher, Mrs. Bass, has an irritating obsession with the metric system. She makes her students measure countless objects, then she writes the measurements on the board. Because Prufrock Prep doesn’t have a class for babies, Sunny becomes Nero’s administrative assistant doing work that a baby shouldn’t.
They are then introduced to Coach Genghis. The Baudelaire orphans immediately recognize him as Count Olaf in disguise but pretend not to recognize him. He makes an unusual remark about how orphans have stronger legs. Then they all rush to the auditorium to listen to Vice Principal Nero’s daily concert, where they are forced, along with the rest of the school, to listen to his six-hour violin playing. At the concert, the Baudelaire orphans decide that they will go to Vice Principal Nero’s office the next day to drop hints about Genghis. However, when they attempt to do this, Coach Genghis enters. The Baudelaire orphans try to unmask him, but he eludes them.
At lunch, Carmelita Spats delivers the message that the Baudelaire orphans are to meet Coach Genghis on the front lawn at sundown (at the time of Nero’s violin concert). Genghis makes them paint a circle, and then run “Special Orphan Running Exercises” or S.O.R.E. laps around the luminous circle at night, for nine days. As the Baudelaire orphans run the laps, they become tired. This causes Violet and Klaus to fail their tests, being too exhausted to be able to tell one end of a metric ruler from another. Sunny is unable to find any staples because she ran out of them.
Then Vice Principal Nero tells the children that if they keep failing their tests, they are going to be tutored by Coach Genghis, and that Sunny will be fired. He says that they will have extra-hard comprehensive exams the next morning. He also demands that they give him nine bags of candy each, as punishment for missing his concerts, and give Carmelita earrings for each time she brought them a message.The Orphans then go see the Quagmires and tell them what happened. Then the Quagmires plot a plan. The Quagmires disguise themselves as the Baudelaire orphans, get a sack of flour to represent Sunny, and do the exercises (at night), for them so that the Baudelaire orphans can study and make staples (Coach Genghis doesn’t know that it’s the Quagmires that are running because it is night time and he can’t see them). The Quagmires leave their notebooks with Violet and Klaus so that they can study. Violet invents a staple-making device (using a small crab, a potato, metal rods, creamed spinach, and a fork) and makes staples while Klaus reads the notebooks.
The next morning, Vice Principal Nero and the two teachers (Mr. Remora and Mrs. Bass) come to the Orphans Shack. They test Violet and Klaus, and give Sunny a stack of papers to staple. Then Coach Genghis arrives. He has discovered, by trying to kick Sunny, that Sunny had been substituted with a sack of flour. Genghis uncovers the Quagmires’ disguises as a result, and gives them canteen duty. The orphans, unable to stand it any longer, attempt to reveal that Coach Genghis is Count Olaf. About that time, Mr. Poe comes to deliver the candy and earrings. Vice Principal Nero tells him that the orphans have been caught “cheating”, and announces that the Baudelaire orphans are going to be expelled.
The Baudelaire orphans tell Mr. Poe that Coach Genghis is Count Olaf. Coach Genghis runs out of the shack, and after the orphans manage to remove his disguise, he succeeds in kidnapping the Quagmires. The two lunch ladies with metal masks are revealed as being Count Olaf’s assistants, the white-faced women, when they remove their masks. The orphans see Olaf’s assistants shoving the Quagmires into an old car. Before they close the door, Duncan yells to the Baudelaire orphans “Look in the notebooks! V.F.D.!” before they are captured.
Unfortunately, Olaf steals the notebooks before they drive away. The orphans are then taken away to be placed with another guardian.
“I would rather eat a bowl of vampire bats, than spend an hour with Carmelita Spats”
“It would be a stroke of luck if Coach Genghis were hit by a truck”
“Don’t worry Baudelaires, don’t feel disgrace, the Quagmire triplets are on the case”
“It’s not particularly wise but it’s a thrill to be disguised.”