The Nautilus is a state-of-the-art submersible-ship which travels across the seven seas, but is specifically available to transport the player across the Indian Ocean at great speed. The ship - and its captain Nemo - are based upon Jules Verne's 1870 Novel Twenty Thousand Leagues Under the Sea.

Captain Nemo built the ship according to his own revolutionary designs, and it is one of the fastest and most powerful ships in the world. Its main purpose is to protect the environment and ward off British colonial influence (which Nemo despises) in the southern hemisphere. Ruthlessly sinking ships and swallowing survivors, the Nautilus has been mythologised as a vicious Sea Monster - however Nemo tries not to kill but rather only capture the sailors and keep them aboard in order to preserve his secret enterprise.

Passepartout and Fogg encounter the Nautilus whilst aboard the Tokoloho, a submersible hunting the mysterious Sea Monster whilst travelling from Bhayi to Saint-Denis. En route they are attacked by the Nautilus and captured. To their surprise, Nemo shows them great hospitality aboard the ship and the conditions are very comfortable. However, their is a price; they can never leave - a conditional Fogg naturally finds unacceptable.

Passepartout, Fogg, and Thabiso and Nthatisi Basia (the owners of the Toholoho) quickly set about repairing their damaged ship in hopes of escaping. Their chance comes when, somewhat ironically, the Nautilus is attacked by a real-life Sea Monster - a giant squid. The Tokoholo manages to escape whilst Captain Nemo goes down with the sinking ship, never to be heard from again.