Arthur Pike, a rebellious 15-year-old who loves online games and hacking, lives with his mum Mary Pike, in an apartment in the Metropolis, Auckland. Mary, a career lawyer had lost since left her marine researcher husband on the Pacific atoll where he had refused to give up his quest for a lost species of deep-sea Nautilus.
Arthur is kidnapped by his reclusive billionaire grandfather, Dr Thaddeus Pike. He is taken to an island in the middle of a brooding lake connected by an underwater cave to the sea. There, in an underground research station, Arthur meets his Nemo-like grandfather for the first time. He is given access to a super computer - and tells Arthur he may one day take over ‘Project Nautilus.’
Arthur’s grandfather has developed a revolutionary organic computer powered (unknown to Arthur) by a giant nautilus which Arthur’s father had finally discovered deep beneath the reefs of the atoll. Dr Pike has connected the creature to the internet, believing that its giant brain will allow him to rule the Web and set the world onto a rational course – his course… But the ‘computer’ is starting to ask awkward questions like “who am I?”
The Nautilus has scientific knowledge, but it wants to be told stories. She wants an identity, a history, and dreams. She wants to learn about joy and sorrow. She is beginning to sound like a child looking for its place in the world....
Arthur is enthralled by the supercomputer, and tells his crazy grandfather he will harness its powers. He is beginning to go over to the Dark Side… But when he breaks into the top-secret basement level of the base, he learns the terrible secret that it is a sea-creature that has been turned into a kind of Cyborg. So Arthur promises the Nautilus he will help it ‘find itself.’
Now the agents of Dr Pike’s deadly rivals, the INC, are closing in on the secret base. They are determined to capture the Nautilus’ secrets by fair means or foul.
Arthur befriends John, the enigmatic caretaker and his daughter Tess who live in the forest on the edge of the lake. Though Dr Pike scorns the caretaker’s ‘Nature worship,’ he needs his massage skills to control his terrible migraines and neuralgia. And Arthur begins to learn of another way besides Dr Pike’s…
Arthur's mother is desperate to get him back. She decides to turn to her estranged husband for help, and he sets sail for New Zealand in his research vessel.
Meanwhile Arthur and Tess develop a bold plan to set the Nautilus free, through the underwater caves to the sea. But it’s not just his grandfather Arthur has to worry about. Dr Pike’s assistant Hilda has her own ruthless agenda - and the INC’s submarine is closing in on Dr Pike’s hideaway.
Dr Pike’s team lose the remote-controlled underwater battle between stingray robots and the INC’s drillerfish, and to protect his secret he pushes a button to terminate the escaping Nautilus in the lake, in a terrible explosion just as the INC frogmen are closing in. Dr Pike and Hilda escape in a submarine as the countdown begins for the detonation of the whole base, as Arthur and Tess escape into the bush, heartbroken at the death of their gentle friend.
However, the Nautilus had a baby (a kind of clone) which she ejected to safety just before she was killed. This baby has all her mother’s memories, though it is small enough for Tess to put it into a goldfish bowl and take it on board when Arthur’s father finally arrives off the coast. Putting out to sea, they are met by two of the giant nautiluses, who had heard of their sister’s plight through the Gaiaweb, and come to rescue her and escort her home. So Tess releases the baby to them, and they wave good bye as the three wise creatures sink into the depths.
But we have not heard the last of Dr Pike – or the INC. The Net Wars are just beginning.