Set in the South Pacific Ocean in the year 1897, beginning right where the original film left off, a larger ship finds a little dinghy with three passengers. They quickly find out that the two adults are dead, but the infant snuggled between them lives- a little two-year-old boy who they assume is named "Richard" since that's the only name he knows. They take the baby aboard and he is given over to the care of the young widow who already has a young daughter named Lilli.
An outbreak of cholera on board pushes the captain to set the widow, two children, and one strong crew member on a smaller boat to save them from the disease. The crew member threatens the children because he thinks they'll endanger the whole group by drinking all the water, and he finds their crying annoying besides. The widow, Sarah, is outraged- she beats the crew member to death and casts his body overboard.
The boat continues to drift until it returns to the island where Richard was born. Huge cresting waves nearly upset the little boat as they come closer to shore, but they arrive safely on the beach. Sarah sets up a little camp against a huge log of driftwood and then the group set off looking for supplies. They find fresh water, fruits and roots while little Richard explores his old stomping grounds. A tropical storm hits, and the three huddle- wet and misrable- in their inadequate shelter. When it abates, Sarah decided to hunt for a more sheltered place to live. They find the little house that Emmeline and Richard (senior) built, and the baby boy runs up the steps looking for his parents. When he finds them missing, Sarah assures him that she will be his mother now.
Life continues, normalcy building as the little family learns to survive. Sarah discovers that every three months, at the full moon, 'heathens' from the north side of the island row in long canoes past the lagoon, and she takes extra precautions to avoid them. Over the next few years, the children grow older, and less clothed, and seem to spend their time exploring the island. Sarah has only two rules: Be home before sunset, and never visit the north side of the island.
She also continually tries to push civilized behaviors on them, teaching them religion, schooling and propiety. While she maintains a 'proper' lifestyle, the children explore themselves and each other, and ask for the facts of life. Sarah dutifully explains the concepts of anatomy, puberty, and marriage.
Later, the children are caught out on the reef while hunting fish, with a huge shark circling the lagoon. It grows dark and Richard eventually throws out the fish they caught to distract the shark and they swim to their drifting boat. Sarah, worried sick, goes out searching for them and finds them just as they drift ashore.
One day a storm blows in part of the roof of the house. After repairing it, Sarah falls deathly ill. She explains to them where and how she is to be buried, and gives them a prayer and script for her tombstone. Sarah then dies and she is buried on an overlook, so that she might see the house and serve as the children's guardian angel. She asks that Richard include his name on her tombstone, even though she is not his 'real' mother. To the end, Sarah wishes that the children remain civilized, and ready for the ship and rescue.
The children are left alone, and the film skips forward several more years. It's Easter, and the teenage Richard (Brian Krause) insists on hunting for eggs, even though teenage Lilli (Milla Jovovich) isn't keen on the idea. Richard promises a prize for the winner, and reminds her that their mother would have wanted them to hunt for eggs. Lilli agrees to play. They both hide ten eggs on different areas of the island, and both find nine. Richard hides one, and lets Lilli win. Her prize is a pearl that she put in her hair with feathers and a twig.
Richard has a continual contention with the shark in the lagoon, the same one that stalked him and Lilli as young children. He brags about his contests against the shark, which Lilli disapproves of. She mocks him, and he mocks her back, because of her fascination with her changing body. They argue, and acknowledge that life if different now that they're older. After a brief friendly interlude, Lilli asks if she could move her bed to another part of the house, instead of sleeping with Richard. "If you weren't going to do it, I was," says Richard
Soon after, Lilli discovers she has gotten her period, and is now a woman. She's thrilled. She's like-wise thrilled when she find out about the fabulous trick Richard can do with his downstairs parts, though he is embarrassed. They bicker, and Richard storms to the other side of the island where he meets the heathens during their ritual. They have a bonfire, and are covered with white paint. Richard slathers himself with black mud to hide, but ends up in a stand off with a heathen. Richard backs off, as does the native, and they go their separate ways- but not before Richard finds blood-soaked leaves on a stone in a clearing. When he finds Lilli again, she is so distraught by his absence that she begs him to never leave her again. Soon after, they exchange primitive rings and pronounce themselves married.
A ship arrives soon after this, their kegs spoiled, in search of fresh water. The couple greets them topless, which is shocking to the captain and crew. "They seem to be an odd mixture of knowledge and ignorance," explains the captain to his pretty daughter Sylvia. "Oh, and their attire is a bit... well, it's quite... sparse." They are also shocked and confused when Lilli cheerfully tells them that Richard isn't her brother, he's her husband.
The captain and his daughter outfit Lilli and Richard in civilized clothing, and the couple makes the crew comfortable on the island. (Well... mostly comfortable). The young pair are used to dining on eel broth and running about naked, but one particular member of the crew doesn't find that quite as shocking. Nor does Sylvia disapprove of anything that Richard decides to do.
Lilli tries to win back Richard from Sylvia (as she sees it) by dressing up and wearing makeup like Sylvia does, and Richard tells her she's being silly. Then Richard leaves to spend time with Sylvia and Lilli goes to wash off the smeared rouge she's applied.
Richard soon learns that Sylvia isn't interested in a platonic friendship, and tells Richard his marriage isn't real and doesn't mean anything. "It does to me," answers Richard. He realizes what Lilli means to him and races off to find her, leaving an outraged Sylvia behind. He arrives in time to find Lilli being accosted by the interested crew member who found her bathing at the pool, and is now hunting for her pearl. A fight ensues, and the man shoots at Richard with his rifle, grazing his arm. The rest of the crew hurries to their aid, but the two men take off sprinting down the beach, the crew member determined to hunt Richard down. They race across the reef and Richard dives into the lagoon. The shark is waiting, as always. Richard out-swims the creature from his years of contests, but the crew member- a poor swimmer- is dragged beneath the water.
When Richard returns, Lilli breaks the news that she won't be returning to civilization on the ship because she is pregnant and doesn't want her baby born into a world with guns. Richard is thrilled, and agrees. The ship sails away at dawn, and the young couple frolics like nothing ever happened to interrupt their blissful existence. Their baby is born, presumably a little girl by the look of the credits.