The narrative begins with a perplexing maritime mystery in eighteen sixty-six, where sailors and governments are terrorized by a gigantic, luminous, and impossibly fast object slicing through the oceans. Professor Pierre Aronnax, a noted French naturalist, joins an American expedition aboard the frigate Abraham Lincoln to hunt down the supposed sea-monster. After a frantic chase and a violent collision, Aronnax, his faithful servant Conseil, and the rugged Canadian harpooner Ned Land are thrown overboard. They discover that the monster is not a living creature at all, but a magnificent and technologically advanced submarine vessel known as the Nautilus.
Captured by the vessel's brilliant and misanthropic commander, Captain Nemo, the three men are told they can never return to the land. Nemo has renounced human society entirely, choosing to live a life of complete freedom beneath the waves where despots and laws cannot reach him. Despite their lack of liberty, the captives are treated to unimaginable wonders, including a vast library, priceless art collections, and cabinets of marine treasures gathered by Nemo himself. The Captain explains the marvels of electric propulsion and the mechanics of navigating the crushing pressures of the deep ocean.
The voyage takes the travellers across the globe, descending into the Indian Ocean, threading through the dangerous Torres Straits, and exploring submarine forests where they walk upon the ocean floor in diving suits. They witness breathtaking marine ecosystems, massive schools of luminous creatures, and the sunken ruins of lost worlds and historical wrecks, such as the remains of La Perouse's expedition at Vanikoro. Along the way, tensions simmer between the captive companions. Ned Land desperately craves escape and fresh terrestrial meat, while Aronnax is utterly consumed by scientific fascination.
As the journey continues into darker and more isolated waters, Captain Nemo's internal torment and fierce hatred of humanity become increasingly apparent. The Nautilus engages in violent encounters with hostile natives, savage sharks, and relentless warships, reflecting Nemo's hidden vendetta. Yet amidst the violence, there are moments of profound sorrow, such as a silent burial in a magnificent submarine coral cemetery. The story weaves together scientific exploration and psychological mystery, hinting at an inevitable and dramatic conclusion to their life beneath the sea.