Chakotay and his sister, Sekaya, are imprisoned on the formerly Cardassian-occupied planet of Loran II. They soon discover that their tormentor is an old enemy: Arak Katal, the Bajoran who betrayed Chakotay's comrades, the Maquis, to Starfleet. Worse still, he is also Chakotay's second-in-command, Lieutenant Andrew Ellis - for he is in fact a Changeling, a shapechanger, a renegade Founder who has been rejected by the Great Link for his evil actions.

On Loran II he has teamed up with Cardassian scientist Crell Moset, who he hopes will restore his Changeling powers to the full. But that is only part of their plan: Moset intends to create a new race, a superspecies to do his will, as the Jem'Hadar serve the Founders. With Chakotay's Sky-Spirit DNA, they may just be able to pull it off - and stopping them could cost Sekaya her life.