The story begins in May 1863, in the Lidenbrock house in Hamburg, Germany, with Professor Lidenbrock rushing home to peruse his latest purchase, an original runic manuscript of an Icelandic saga written by Arne Saknussemm. While looking through the book, Lidenbrock and his nephew Axel find a coded note written in runic script which, when translated into English, reads:
Descend, bold traveller, into the crater of the jökull of Snæfell, which the shadow of Scartaris touches (lit: tastes) before the Kalends of July, and you will attain the center of the earth. I did it. Arne Saknussemm
Professor Lidenbrock leaves for Iceland immediately, taking his reluctant nephew with him. In Iceland they hire Hans Bjelke as their guide. Axel repeatedly tries to reason with him, but Professor Lidenbrock will not listen.
In late June, they reach the volcano, which has three craters. According to Saknussemm's message, the passage to the center of the Earth is through the one crater that is touched by the shadow of a nearby mountain peak at noon, during the last days of June. On the second to last day, the sun comes out and the mountain peak shows the correct crater to take.
After descending into the crater, the three travellers set off into the bowels of the Earth, encountering many strange phenomena and great dangers, including a chamber filled with combustible gas, and steep-sided wells around the "path". After taking a wrong turn, they run out of water and Axel almost dies, but Hans taps into a neighbouring subterranean river. Lidenbrock and Axel name the resulting stream the "Hansbach" in his honour and the three are saved.
After descending many miles, following the course of the Hansbach, they reach an unimaginably vast cavern. This underground world is lit by electrically charged gas at the ceiling, and is filled with a very deep subterranean ocean, surrounded by a rocky coastline covered in petrified trees and giant mushrooms. The travelers build a raft out of trees and set sail. The Professor names this sea the Lidenbrock Sea. While on the water, they see several prehistoric creatures such as a giant Ichthyosaurus, which fights with a Plesiosaurus and wins. After the battle between the monsters, the party comes across an island with a huge geyser, which Lidenbrock names "Axel's Island".
A lightning storm threatens to destroy the raft and its passengers, but instead throws them onto the coastline. This part of the coast, Axel discovers, is alive with prehistoric plant and animal life forms, including giant insects and a herd of mastodons. On a beach covered with bones, Axel discovers an oversized human skull. Axel and Lidenbrock venture some way into the prehistoric forest, where Professor Lidenbrock points out, in a shaky voice, a prehistoric human, more than twelve feet in height, leaning against a tree and watching a herd of mastodons. The three wonder if the creature is a man-like ape, or an ape-like man. The sighting of the creature is considered the most alarming part of the story, and the explorers decide that it is better not to alert it to their presence as they fear it may be hostile.
The travellers continue to explore the coastline, and find a passageway marked by Saknussemm as the way ahead. However, it is blocked by what appears to be a recent cave-in and they blast the rock with gun cotton and paddle out to sea to escape the blast. Behind the rockfall is a seemingly bottomless pit, and the travellers are swept away as the sea rushes into the pit. After spending hours being swept along at lightning speeds by the water, the raft ends up inside a large volcanic chimney filling with water and magma. Terrified, the three are rushed upwards, through stifling heat, and are ejected onto the surface from a side-vent of a volcano.
When they regain consciousness, they discover that they have been ejected from Stromboli, a volcanic island located in southern Italy. They return to Hamburg to great acclaim – Professor Lidenbrock is hailed as one of the great scientists of history, Axel marries his sweetheart Gräuben, and Hans eventually returns to his peaceful life in Iceland. The Professor has some regret that their journey was cut short.
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