The Baudelaire orphans and Count Olaf flee the burning Hotel Denouement after burning it down. After surviving a storm, they find themselves on a coastal shelf of an island inhabited by a mysterious group of people. They are first greeted by a little girl, Friday. Count Olaf, who had previously proclaimed himself king of Olaf-Land, threatens the girl with a harpoon gun. Friday is unfazed; she refuses Olaf permission to land on the island, but invites the Baudelaires onto the island. Along the way, she describes what the islanders do with their time—all year long, they build an outrigger on the coastal shelf, and once a year the water rises high enough to submerge the shelf and launch the outrigger. This is known as Decision Day, when anyone who wishes can board the ship, bite a bitter apple, spit it back out, and sail away. The island facilitator, Ishmael, introduces the Baudelaires to the strange island customs. Also, Ishmael has the islanders (most named after famous literary or historical castaways) introduce themselves to the Baudelaires.
Ishmael, according to the islanders, injured his feet a long time ago and, consequently, must keep his feet submerged in clay. Every time there is a storm, the residents of the island go out to the coastal shelf to pick up items that have washed up that may be useful. These items are judged by Ishmael. If he decides that the items are not useful, they are loaded onto a sled and towed by a local herd of sheep to a local arboretum, where no one should go (according to Ishmael) lest they injure themselves amongst the garbage. The sheep and the sled are also Ishmael’s main method of transportation.Although Ishmael always tells the islanders “I won’t force you”, it soon becomes apparent that his decisions go largely unquestioned and his suggestions are obeyed as if they were orders. After the Baudelaires introduce themselves, Ishmael toasts the “Baudelaire orphans” (despite their not having mentioned their lost parents) with the coconut cordial which everybody carries, but which the orphans themselves dislike.
After another storm, more objects wash up including a giant pile of books tied together in the shape of a cube, an unconscious and pregnant Kit Snicket, and the Incredibly Deadly Viper from Uncle Monty’s collection. The islanders arrive and Count Olaf tries to fool them by disguising himself as Kit Snicket (with the diving-helmet containing the Medusoid Mycelium tucked under his dress as his supposed baby). However, the islanders immediately see through Olaf’s disguise and cage him. They then debate whether the orphans should be expelled from the colony when they discover that the Baudelaires are carrying “contraband” items. Ishmael decides that the children, Kit, and Olaf should all be abandoned unless they agree to abide by the colony’s rules. The children, along with Olaf, are left on the coastal shelf. After everyone leaves, Olaf tries to tempt the children to let him out of the cage by promising to explain the many mysteries and secrets which they have been surrounded by since The Bad Beginning, but they ignore him.
That night, two of the islanders, Erewhon and Finn, sneak out to feed the children and ask them a favor. A group of discontented colonists are planning a mutiny against Ishmael in the morning, and they ask the Baudelaires to go over to the arboretum where all the contraband items are collected, and find or make some weapons to use in the rebellion. The mutineers refuse to help Kit unless the Baudelaires help them. The children agree, and set off for the arboretum. Upon arrival, they notice very strange clay-encrusted footprints leading to the arboretum. They conclude that Ishmael has been getting up during the night and sneaking out to the arboretum on his perfectly healthy feet to eat apples. As they move to the center of the arboretum, the orphans discover a well-appointed living area, before they are in turn discovered by Ishmael. They learn that their parents were once the island’s leaders and were responsible for many improvements meant to make island-life easier and more pleasant, but they were eventually overthrown by Ishmael, who believed that a strictly-enforced simple life (combined with the opiate of the coconut cordial) was the best way to avoid conflict. The Baudelaires find an enormous history of the island, entitled A Series of Unfortunate Events, written by the many different people who had served as island leaders, including their parents and Ishmael. Ishmael also makes references to many other people, including a girl with only one eyebrow and ear (the mother of Isaac Anwhistle) and Gregor Anwhistle.
The Baudelaires and Ishmael go back to the other side of the island, where the mutiny is already underway. Count Olaf returns, still in disguise. After a brief exchange, Ishmael harpoons Olaf in the stomach, also inadvertently shattering the helmet containing the Medusoid Mycelium, infecting the island’s entire population at once. With Count Olaf slowly bleeding to death, the Baudelaires run back to the arboretum to try to find some horseradish to cure everyone. They learn that their parents had hybridized an apple tree with horseradish, allowing the fruit to cure the effects of the Medusoid Mycelium. After sharing the apple and curing themselves, they then gather more apples for the island’s inhabitants, only to discover that the island people have abandoned the mutiny and boarded their outrigger canoe, ready to set sail. Ishmael refuses to allow the apples on-board, though it is clear that he himself has already eaten one to cure himself, and the boat sails away to a horseradish factory to save everyone (It is hinted though, that one apple might have been sneaked on board by the Incredibly Deadly Viper to tide them over until they reach the factory).
Kit tells the Baudelaires the fate of the Quagmires, Hector, Phil, Captain Widdershins, and his two stepchildren Fernald and Fiona. After reuniting on Hector’s float, they are attacked by trained eagles, who pop the balloons supporting the float and send them hurtling back to the ruins of the Queequeg. There, they are taken by the mysterious object shaped like a question mark (called the “Great Unknown” by Kit Snicket). In turn, the Baudelaires confess their own crimes committed at the Hotel Denouement. At this point, Kit is about to go into labour. She seems to be dying of the fungus, but cannot eat the bitter apple due to the hybrid’s unhealthy effects on unborn babies. She is still trapped on top of the cube of books (her Vaporetto (boat) of Favorite Detritus) but when the critically injured and fungus-choked Olaf hears that she is still alive, he takes a bite of an apple and manages to get her safely down onto the beach, giving her a single soft kiss as he lays her on the sand and collapses, still conscious, beside her. Kit recites the poem “The Night Has a Thousand Eyes” by Francis William Bourdillon, answered by Olaf reciting the final stanza of Philip Larkin’s “This Be The Verse”, who dies soon afterward. The Baudelaires help Kit give birth to a baby girl. Kit then dies due to the Medusoid Mycelium, after asking the orphans to name the baby after their mother. The Baudelaires become Kit’s child’s adopted parents, and became the only ones in the island. They bury Kit and Olaf next to each other somewhere on the island.
Unlike the previous installments in the series which each have thirteen chapters, The End features a total of fourteen chapters. Chapter Fourteen is featured as its own book within The End, serving as an epilogue to the series.One year later, Kit’s baby and the Baudelaires sail away from the island on the boat they came on to immerse themselves in the world once more. As they board the ship, Kit’s baby says the boat’s actual name, “Beatrice,” which is also her own name.There is an author and illustrator page, as usual, and a final image which depicts a lonely sea with the murky shadow of a question mark in the water. The author and illustrator page was the only instance that artist Brett Helquist and Lemony Snicket swapped their billing places in the pictorial credits. Brett, dressed in Snicket’s usual fashion, was photographed and on top, while Lemony, face exposed save for cucumber slices over his eyes, was drawn underneath—a comic depiction of Snicket, as he is shown relaxing beside a pool with a cocktail, when he (as are the Baudelaires) is usually depicted as terribly unfortunate. Their roles revert to their traditional billing places at the true conclusion of the book. Brett Helquist is illustrated and Snicket holds a stack of papers hiding his face with a description saying that he is still at large.