The Battle of Richmond, March 20, 1865: Captured by Confederate forces, the group escapes their captors and flees in a helium balloon. Rising into the sky, the travelers and their balloon are carried away by strong winds and soon find themselves over open water.

Attempting to land, the balloon descends uncontrollably (helped along by Nemo observing from an island below) forcing the group to climb into the rigging and drop the backet to remain aloft in hopes of reaching the island before they plunge into the ocean. Struggling to stay in the air, Captain Harding sacrafices himself to the ocean, allowing the balloon to slow its descent and reach the island.

Exploring the island for signs of civilization with Neb, Herbert becomes trapped in a rock pool as the tide comes, threatening to drown him. Neb manages to rescue Herbert (with unseen help from Nemo). Herbery and Neb enter into a cave where they encounter signs of habitation.

Herbert and Neb find Captain Harding alive in the cave but he has no memory of how he got there, only of slipping below the waves after jumping from the balloon. Reunited, Harding, Spilett and Neb decide to climb to the top of a mountain to get their bearings. Along the way they stop at a pool where Spilett takes a swim only to get attacked by an unseen creature, eventually escaping to the safety of the shore (with help from Nemo). Meanwhile, Jack and Herbert go off hunting but Herbert can't bring himself to kill. They come across a cave and inside they find an alter and a gold plate. They become trapped when the entrance closes up. Unable to dig their way out and with hope seemingly vanishing, a green light (Nemo) draws their attention to an underwater exit that leads them back to the sea and the arms of their companions.

Following an earthquake, the group decides to seek shelter further inland. When a landslide strikes, Gideon becomes trapped beneath some large boulders. Harding and Neb set out to find materials to make an explosive change but Neb is overcome by sulfur fumes and must be pulled to safely by Harding. The final item on Cyrus's list turns up out of thin air (Nemo) allowing him to formulate an explosive to free Gideon. Traveling on, Neb falls down into a cave complex which becomes the group's new home, christened "Granite House" by Gideon. While fishing, Neb and Herbert pull an old sea chest out of the ocean. Returning to camp for asistance, Neb is hit by the effects of eating wild berries and loses his sight while atop a dangerous precipice and loses his footing…

Neb is rescued when a vine is lowered to him, although when Captain Harding and Herbert arrive, both deny being responsible. For Harding, it is another sign that they are not alone on the island. When the sea chest is brought back to Granite House it is found to contain a wealth of ship building tools and other supplies. Eager to get to work on a new boat, the group set out to look for materials and come across the remains of their balloon. Transporting it back down river, their raft overturns in the rapids and washes Pencroft, Gideon and Neb towards a raging waterfall. When all hands are safely rescued, the castaways return home to discover their home has been visited while they were away. Herbert and his father take their new boat out on its maiden voyage but encounter an unknown force at sea that pulls Herbert overboard…