Captain Chakotay and his sister, Sekaya, are being held captive beneath the surface of Loran II by a Changeling – an outcast Founder masquerading as Chakotay's second-in-command, Andrew Ellis. To Chakotay's horror, the Changeling gives the two prisoners over to the infamous Cardassian scientist Crell Moset, who plans to use Chakotay's Sky Spirit-enhanced DNA to create a superior species that will bring him the fame and acceptance he craves.

Leaving Chakotay and Sekaya to their fate, the Changeling assumes Chakotay's identity and infiltrates the Starship Voyager, putting the entire crew at risk. Dr. Jarem Kaz and Lieutenant Harry Kim, increasingly suspicious of their captain's odd behavior, turn to Admiral Janeway and Lieutenant Commander Tom Paris for help. As Paris races to save Voyager from catastrophe, the real Chakotay must undertake a "Spirit Walk" that could set him and his sister free – or lead to their ultimate destruction.