In the final days of the Civil War, a Union captain, a freed slave, a reporter, and a family of man, wife, and son, escape from the Confederates in a stolen balloon which drifts across America and finally deposits them on a Pacific island.
Harding and company learn their island lies far from any mainland, is volcanic in origin, and seems prone to earthquakes. They also come to believe it's inhabited by some sort of force or power characterized by a green light.
A rockslide of suspicious origin partially buries Gideon. To free him, Harding creates an explosion using improvised gunpowder. Later, Neb stumbles into a cave which the castaways decide to turn into a residence: Granite House.
Discovery of a washed-ashore chest full of carpentry tools and navigation instruments inspires the castaways to build a boat. For a sail, they'll use cloth from their balloon which they find tangled in a tree.
The castaways find a note and message in a bottle. These lead them to an elusive, possibly dangerous man named Ayrton who's been stranded on the island for six years. One of the castaways then apparently dies of a snakebite.
Tensions and misunderstandings grow between the castaways and the island's mute, bearded hermit who may have slit the throats of several of the island's goats. Suspicion lingers, however, that there's yet another presence on the island.
Pirates land on the island, taking the castaways by surprise. The pirates seek to recover buried treasure and their arrival prompts the release of new and disturbing information about the hermit, Ayrton.
The pirate, Cutler, survives a mysterious explosion on board his ship. He then wreaks havoc on the island, grazing Herbert with a bullet and shooting Jack with a poison dart before his reign of terror is brought to an end.
Harding's underwater explorations lead him into a metallic chamber where he talks to (but does not see) the island's mysterious Phantom. In Granite House Gideon confronts a young black woman whom he regards as a savage cannibal.
Harding returns from talking with the Phantom, discovers a party of "cannibals" has landed to retrieve the young woman who confronted Gideon. Hostage-taking ensues. The "cannibals" finally depart, refusing to take the castaways with them.