Five prisoners of war during the Civil War escape in a hot air balloon: Captain Cyrus Harding, Neb (Harding’s servant), Gideon Spillet (a reporter), Jack Pencroft (a sailor), and Herbert Brown (a fifteen-year-old boy). The balloon flying off wildly finally lands near an island where the five members of the balloon survive and eventually find each other.

The men at this point are busy making a home for themselves on the island because they do not know when they will be rescued. They name the island Lincoln Island. By all measures, the island flourishes. Harding, as a military engineer, know nearly everything (without exaggeration). Much of the book is devoted to showing the ingenuity of Harding and the other men.

All is well until the colonists (that is what they call themselves) see a pirate ship; a battle ensues. In a mysterious way, the pirate ship explodes, but a number of pirates survive, and they attack the colonists. Herbert is wounded.

While the battle is still going on, the colonists receive a mysterious telegraph to go to a hidden cave. When they get there, they meet the famed captain Nemo. They also find out that he was the one who destroyed the pirate ship. Moreover, they also find out that it was he who mysteriously aided them. Nemo asks the colonists to bury him in his submarine, as he is dying.

The colonists build a boat and escape the island, and eventually they are rescued by a ship called the Duncan.