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.

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…

Jack leaps into the water to rescue his son from the unseen menace and they swim to the safety of the shore where Gideon has found a bottle. Back at Granite House a message is pulled from the bottle‹written by a fellow castaway on the island! Jack, Herbert and Gideon set out on a test voyage in their boat to locate the castaway. They find his well-stocked camp and gather up supplies as no one is in sight. Mr Ayrton soon makes an appearance and Herbert convinces his father to take him back with them. Meanwhile, Joanne, while out by herself gathering plants, is overcome by Nemo's gas devise and falls unconscous. When Neb goes to search for her, he too is overcome but before he collapses, he sees Nemo approach. Back in Nemo's lair, Nemo posions Neb, making it appear to be from a snake bit. Harding later finds Neb's body and a memorial service is held, with Harding biding a tearful farewell to his dear friend.

While the castaways grieve for Neb, Nemo revives him and puts him into suspended animation storage. Pencroft's jealousy leads him to hunt down Ayrton. Harding soon realizes the phantom presence on the island is causing the castaways to turn against one another.

Pirate Captain Cutler and three of his crew come to the island to collect their buried treasure and seek revenge on Ayrton, whose dark past is revealed.

Joanna stumbles into an underwater trap set by Nemo and the others race to free her. Shortly thereafter, Captain Cutler, sole survivor of his ship's destruction, makes his presence known on the island and leaves a violent wake as he seeks revenge on the castaways.

Harding dives into Nemo's lair beneath the lake and is trapped in a chamber. Gideon is awakened by an intruder.

A tribe of native Islanders arrive on the island in search of Nui, a young native girl they believe has special significance.

Nemo observes Harding's feelings about Joanna, manifested in romantic dreams, as part of his research into the workings of the human mind. Meanwhile, Joanna is trapped by an earthquake while Herbert discovers a cryptic note from Ayrton.

Nemo intercepts a canoe and brings a wise old native woman to the island as a culture clash experience, but finds himself face to face with a superior power. Joanna's stand for women's rights has unexpected consequences.

Nemo fulfills a promise to Katira to bring the rest of her people to the island, then watches with glee as the natives take over Granite House and send the castaways into exile.

A tattooed native man arrives on the island telling the castaways that he is on a spiritual quest. Nemo is delighted when his presence has a disruptive influence on the group.

Herbert realizes that it is his birthday, but decides to keep it a secret. He is angry because he thinks Joanna has forgotten, and while she prepares a surprise gift for him, he decides to find a way to leave the island.

When pirates bring two women to the island, Nemo uses the situation to study human mating habits. The women, meanwhile, set their sights on Gideon and Herbert, which encourages the men into a near fatal show of male bravado.

Joanna argues with Herbert after a dream about a baby, and leaves the Granite House, headed for Ayrton's cabin. She has an accident on the way there, and is rescued by Nemo, who drugs her and questions her, learning she is pregnant with Jack's baby, but is afraid of childbirth.

Nemo's hidden camera in Granite House breaks down, so he disguises himself as a shipwrecked Englishman in order to gain admittance into the house to fix the equipment.

A series of accidents leads Harding to come face to face with the mysterious phantom, and he struggles with how to share the shocking truth.

The castaways share their experiences with the phantom and realize he may be their only hope of escaping the island.

Nemo reveals to Harding that his need to complete his experiment is greater than his desire to help the castaways off the island, and Harding is forced to cut a deal.

Harding carries out his part of the deal with Nemo, and the other castaways are enraged, moving from the Granite House into a makeshift hut on the beach, and prompting Nemo to announce his experiment is complete.

Harding carries out his part of the deal with Nemo, and the other castaways are enraged, moving from the Granite House into a makeshift hut on the beach, and prompting Nemo to announce his experiment is complete.