Crusoe's identity crisis goes through several stages. At first, he loses all sense of self, stripping naked, letting his hair grow long, and wallowing in the mire of the island's swamps. He comes close to losing his humanity and simply becoming a mad, wild creature.

In his second phase, he takes hold of himself, and keeps his madness at bay by, like Defoe's Crusoe, dominating the island in a rigidly structured way. He invents a "clock" that measures time through drips of water, cultivates grain crops, domesticates goats, and builds a house he calls the Residence. In the second phase, in an almost manic desire to dominate, he establishes a rice paddy, writes laws full of punishments should he transgress, and establishes a military barricade after he sees cannibals visiting the island.

In a third phase, he climbs into a small crevice deep in a cave to get rid of all light, and in that place faces life and death, is tempted by death, and yet chooses life, emerging reborn. At this point he attempts oneness with the island, primarily through having sex with it.

The fourth phase occurs when he meets Friday, first dominating him as his master, and then coming fully into his own in a peaceful oneness with both the island and Friday.

Tournier explores what it is to be human without other humans to define us, and argues that we cannot experience our full humanity without other people. Robinson cannot become his best and fullest self until he finds companionship with Friday and—most importantly—until he can respect Friday as equal, a fellow human who has something to teach him and not simply a living object he can use.

The novel also explores what constitutes a utopia and rejects the idea that it comes from dominating nature and creating a "little Europe" in another place. That kind of society is restrictive and punitive. Crusoe cannot create a utopia through either sex with the island or dominating Friday. An utopic space is cleared for Crusoe when Friday accidentally destroys his rice paddy and then accidentally blows up much of what Crusoe has built. It is then, unencumbered by meaningless possessions, that Crusoe can enter into a harmonious relationship with the island and Friday. Utopia occurs, Tournier says, when we transcend ideas of domination.