The First Officer is a complex – some would say difficult – man. His background is unique: he spans two cultures, one foot in each, belonging to both and yet to neither. In the twenty-second century, a group of Indian traditionalists became dissatisfied with the "homogenization" of Humans that was occurring on Earth. Strongly motivated to preserve their cultural identity, they relocated to a remote planet near what has now become known as the Demilitarized Zone.

Chakotay is a member of that Indian nation, but was always what his people call a "contrary;" he had a mind of his own, an individualistic rather than communal way of thinking. Though proud of his heritage and his traditions, he was not satisfied to ignore the galaxy around him – a galaxy teeming with diverse life-forms and amazing technology. He broke from his people, educated himself in the ways of the twenty-fourth century, and attended Starfleet Academy.

But he was "contrary" at the Academy, also, and found he had difficulty adhering to the rigid codes and rules. He was commissioned and posted to the Merrimac just after the end of the Cardassian wars. When he learned that his people were becoming victims of attack by Cardassians, he left Starfleet to defend them, joining the then-infant group, Maquis. Chakotay never gave up his practice of traditional rituals, and he preserves them aboard Voyager. In his quarters is an Indian altar and other traditional ritual items. One wall contains a version of traditional mural art. He visits the Holodeck where he has a "habak" program for the celebration of his people's ceremonial cycle.

As an adolescent, Chakotay pursued a vision quest, and in doing so obtained a "spirit guide" – a timber wolf – which appears to him now in dreams and visions, and often guides him in his decision-making process.

He has a reverence for all living things, and when he eats he offers thanks to the earth for providing food; he will not eat meat; he takes no drugs or alcohol.

As a leader he is steady, fearless, and capable of inspiring absolute devotion. Though he comes onto Voyager more by necessity than choice, he quickly wins the respect of even the most die-hard Starfleet veterans. He strikes an immediate and powerful bond with Janeway, and an unusual one with Kim, who through Chakotay's example begins to question his own homogenization and the loss of his traditional values.

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