While Kes chides the Doctor for his lack of compassion towards the discomforts experienced by pregnant Ensign Wildman, Chakotay is surprised to discover symbols on an alien moon that are strikingly similar to ones he observed as a teen in the Central American rainforest. At that time, he'd been accompanying his father, Kolopak, on a journey to find the truth about their ancient ancestors. Intrigued, Chakotay is permitted to lead an Away Team to the site. It might provide some answers — or, failing that, some of the minerals that the ship badly needs for repairs.
The Away Team beams down to what appears to be the uninhabited planet. As they prepare to land their shuttlecraft, Chakotay remembers back to the age of 15 when he disappointed his father by not embracing the traditions of his tribe. The memories are strong as the team explores the planet's terrain. But before he can absorb any comparative implications, Neelix is injured by a native hawk, and later Tuvok finds what appears to be an abandoned village.
Thinking the Away Team may have frightened off the natives, Chakotay advises Tuvok and Torres to lay down their weapons in a gesture of trust. Instead, the gesture seems to inspire a violent storm. Tuvok and Torres beam back up, but Chakotay is left behind, knocked unconscious by a falling tree.
Later, Janeway is frustrated by several unsuccessful attempts to find Chakotay — it's almost as if something on the planet is trying to prevent them from beaming down. As they try to enter the planet's atmosphere, they're engulfed in a cyclone which Tuvok suspects is generated by residents to ward off intruders.
When Chakotay recovers, he finds the inhabitants of this strange world, and is surprised to learn that they speak the language of his ancestors. They recognize the symbol tattooed on Chakotay's forehead, which he wears to honor his father, who wore it to honor his ancestors. The inhabitants say they knew those ancestors — "the Inheritors" — when they visited Earth some 45,000 years earlier.
Chakotay realizes that these are the "Sky Spirits" which his people's lore is based upon. The aliens visited Earth again much later, and discovered that nearly all traces of the Inheritors had vanished, presumably destroyed by other humans. The aliens tell Chakotay that they attacked Voyager and its crew with storms because they feared they were enemies who would try to destroy them just as the human ancestors did to the Inheritors. Chakotay assures them that humans have come a long way since those ancient days and mean them no harm. The storms vanish and the ship is saved just in time. After the aliens give Chakotay some of the minerals that Voyager needs, they bid him farewell, leaving Chakotay with the feeling that he's recovered his connection to his people — and his father.