Everwild continues the stories of Allie and Nick as they pursue separate goals. Allie sets off with Mikey, who was once the terrifying monster, McGill, in the book Everlost, to find her parents in hopes that she might put her spirit to rest; meanwhile, Nick finds himself in a race against time to save the Afterlights from endless entrapment in Everlost by the Sky Witch, Mary Hightower. Traveling in the memory of the Hindenburg, Mary spreads her propaganda and attracts Afterlights to her cause at a frightening speed.
Nick, in control of a train, is heading south to gather his own support against Mary. Due to the rumors Mary has spread about the Chocolate Ogre Nick is being overwhelmed by the memory of the chocolate stain on his face, and he is unable to stop the chocolate from spreading over his body. Nick follows the rumor of "Zack the Ripper", revealed to be Zinnia, a girl who died in the Civil War while pretending to be a boy. Zinnia has the ability to "rip," breaking the barrier between the living world and Everlost to pull or push things through. With her abilities, Nick begins to devise a plan to confront and defeat Mary.
Meanwhile, together with Mikey, Allie the Outcast travels home to look for her parents and her own life. Along the way, Allie meets a three other skinjackers, lead by Milos. Allie is tempted by the seductive thrill of skinjacking as she masters the skill, until she discovers the shocking truth about skinjackers: skinjackers are not necessarily dead or alive. Allie's body lies in a comatose state waiting for her soul to rejoin it, and she has the choice whether to remain a skinjacker in Everlost or return to her living body. Mikey discovers that, though he is no longer a monster, he retains the ability to morph himself into monstrous creations of his own mind. Mikey grows jealous of Milos's relationship with Allie. Allie and Mikey part ways with the skinjackers, who Mary later joins forces with.
By the end of the book, The Ripper, Allie, and Nick join forces to defeat the evil Mary Hightower and foil her plan to kill all the world's children in order to bring them into Everlost. Nick and the Ripper arrange to meet Mary at a vortex in Graceland, and Zinnia uses her abilities to push Mary into an opening that takes her into the real world. On her way through, Mary manages to grab onto Zinnia and pull her in with her. The vortex's power causes Nick succumbs to memory and becomes a fully chocolate puddle. The skinjackers, now on Mary's side, blow up a bridge in the living world so the Mary's army can cross over to the unknown land west of the Mississippi River. Allie is captured and strapped to the front of the train. Mikey painstakingly shapes Nick's chocolate puddle into a golem that retain none of Nick's memories or intelligence. Determined to follow Allie, Mikey sinks into the earth with the chocolate golem so that they can cross into the west. Milos meets Mary in the real world, where she asks him to kill her so that she can return to Everlost and continue her crusade.