One year has passed since the ancient spirits Discord and Nocturne returned to the world. Life has returned to normal for Thistleroot and his new friends, or at least as normal as it ever gets in Equestria. After receiving a job offer from Princess Celestia to research new kinds of fauna, he, Scootaloo, and Mimic, return to Greenhaven Grotto, and the newly unsealed Libiris.

What should have been a simple research assignment turns into more than any of them bargained for: ancient spirits, forgotten species, and a war between immortals that once threatened the entire world.