The third installment in the Fablehaven series continues the story of siblings Kendra and Seth Sorenson, who spend their summers at Fablehaven, a secret wildlife preserve for magical creatures managed by their grandparents, Stan and Ruth Sorenson. Kendra became fairykind the previous summer, gaining abilities such as perceiving hidden magic and understanding fairy languages. This volume splits its narrative between a mysterious plague transforming Fablehaven's creatures of light into beings of darkness and Kendra's dangerous mission to a distant preserve in Arizona.
While sneaking into the woods to trade batteries to the satyrs Newel and Doren, 12-year-old Seth discovers trouble inside the Seven Kingdoms of the nipsies, half-inch-tall fairy folk who build miniature cities inside a hollowed-out hill. Two kingdoms have turned warlike, their citizens transformed with gray skin, red eyes, and fangs, claiming allegiance to a mysterious new master. Seth reluctantly reports the discovery to Grandpa, earning punishment but providing the first warning of a spreading corruption.
Meanwhile, Kendra broods over a message from Vanessa Santoro, a narcoblix (a creature who bites victims to control them in their sleep) and a former ally now imprisoned in the Quiet Box. Vanessa accuses the Sphinx, the most trusted ally of the preserves' caretakers, of secretly leading the Society of the Evening Star, the enemy organization seeking to open Zzyzx, the great demon prison. The accusation remains unverified when Warren Burgess, an adventurer, and Tanu, a Samoan potion master, return from separate investigative missions with no concrete evidence.
Warren also reveals that the Knights of the Dawn, a secret brotherhood combating the Society, are holding a rare gathering, and the masked Captain has requested Kendra's induction. Though the group fears a trap, they decide Kendra must attend to avoid arousing suspicion. At the gathering, Kendra is inducted alongside Gavin Rose, a teenager whose dragon-expert father was killed by a dragon. Their Lieutenant, Dougan Fisk, assigns Kendra to travel to Lost Mesa, a secret preserve on Navajo land in Arizona, to help recover one of five artifacts that together could open Zzyzx. Warren privately tells Kendra he plans to steal the artifact from Dougan afterward to prevent any single person from controlling multiple artifacts, and Kendra agrees.
At Fablehaven, dark fairies attack Seth in the yard. These creatures are not in a traditional "fallen" state, which would bar them from protected areas, but in an unprecedented "darkened" state that preserves their access. When Tanu and Coulter Dixon, a magical relics expert, encounter dark fairies in the woods, Coulter vanishes instantly upon contact. The group consults Vanessa, who suggests the prisoner the Sphinx freed from the Quiet Box may have been released onto the preserve, making that prisoner the plague's likely source.
At Lost Mesa, Kendra's group struggles to find a path up Painted Mesa, an ancient plateau housing the artifact's vault. During a violent rainstorm, Kendra's fairykind sight reveals the Flooded Stairs, a legendary pathway unseen for centuries, and she leads the group up the treacherous steps. At the summit, kachinas, powerful nature spirits, attack. Neil, the group's Navajo guide, reveals himself as a skinwalker (a person who can transform into an animal) by becoming a stallion to rescue Kendra and Gavin. Inside the vault, the group navigates floating chokepods, bulbs that release lethal gas if touched. Neil dies after brushing one, and Gavin tames a young copper dragon through eye contact. When they reach the innermost chamber, they find no artifact. Kendra reads an inscription in a secret fairy language: Patton Burgess, the legendary former caretaker of Fablehaven, relocated the artifact there long ago.
Back at Fablehaven, the plague escalates. The transformed satyr Newel bites Tanu during a confrontation, and the shadow spreads until Tanu becomes a shadow person like Coulter. Seth discovers he alone can see the shadow people, a consequence of his previous encounter with a revenant, an undead guardian, which also left him immune to magical fear. Defying Grandpa, Seth follows the shadows to the lair of Graulas, one of Fablehaven's most powerful demons. While Grandpa stands paralyzed by the demon's aura, Seth converses freely with Graulas, who reveals the prisoner was Navarog, the demon prince and lord of dragons. After being freed, Navarog retrieved the dark nail Seth had once pulled from the revenant and delivered it to Kurisock, a demon of shadow bound to a tar pit on the preserve. The nail amplified Kurisock's power, enabling the plague.
When Kendra and Warren return with news that the artifact is at Fablehaven, the crises converge. The brownies, small creatures who maintain the house, have been corrupted and seize control, booby-trapping the building and stealing the register that controls the preserve's boundaries. The family flees to the pond surrounding the Fairy Queen's shrine, where magic repels dark creatures.
Lena, a naiad (water spirit), once became mortal to marry Patton before returning to the pond. Kendra persuades Lena to reveal the artifact's location: a safe in the old manor appearing every Monday at noon for one minute. A raid on the manor fails when Ephira, a spectral woman haunting the building, paralyzes Grandpa, Grandma, Warren, and Dale, the family's groundskeeper, with supernatural dread. Only Seth, immune to magical fear, reaches the safe and recovers the Chronometer, a golden sphere with power over time. Pressing its buttons inadvertently summons Patton Burgess himself, transported forward from his own era.
Patton defeats the centaur Broadhoof in a duel to cancel a debt of honor Seth recklessly incurred, and his presence draws Lena from the water. She leaps from the pond carrying a silver bowl from the Fairy Queen's shrine, choosing mortality again for three days with her husband. Patton reveals the plague's origin: Ephira was once a hamadryad (tree nymph) who married his uncle Marshal Burgess and renounced immortality. When Marshal betrayed her, the devastated Ephira struck a bargain with Kurisock, cutting down her bonded tree and bringing its last seed to the demon. Kurisock bound himself to the seed and through it to Ephira, transforming her into something dark. With the nail now embedded in the cursed tree, the demon's power flows through Ephira, making the darkness contagious.
Kendra visits the Fairy Queen's shrine, where the Queen confirms Kendra's status as her handmaiden with authority to command fairies. The Queen forges a talisman, an egg-shaped white pebble, by concentrating the shrine's protective energy into a single object, permanently destroying the shrine. If the talisman touches the nail, both will be destroyed, but whoever connects them will die.
Kendra's touch restores shadow-Coulter, and the group marshals the preserve's remaining light creatures for a final assault. At Kurisock's tar pit, battle erupts against corrupted creatures. Ephira's tendrils of dark fabric transform allies and kill the centaur Broadhoof, who is trapped between the talisman's light and Ephira's darkness. When Patton tries to throw the pebble at the nail, the two objects repel each other, and Ephira seizes Patton, turning him invisible. Lena catches a throw from Kendra, forces her way to the cursed tree, and presses the pebble against the nail. A shock wave radiates outward, destroying both objects. Ephira crumbles to dust, Kurisock dissolves, and the plague reverses across the preserve. Lena lies dead at the base of the shattered tree.
All darkened creatures are restored, and the imprisoned family members are found unharmed. Patton grieves for Lena but resolves to return to his own time and love her fully for the rest of their life together. Dougan confirms that the Sphinx is the Captain of the Knights and a traitor; when confronted, the Sphinx escapes using a teleportation rod Kendra had unknowingly recharged. Lost Mesa has also fallen: The dragon Chalize escapes, museum skeletons are reanimated, and zombies break free. Before departing for his own era, Patton tells Kendra his Journal of Secrets contains hidden messages written in umite wax, a concealed medium readable only with her fairykind abilities, and that information about two more artifacts lies in a chamber beneath Fablehaven's dungeon. Kendra heads home carrying the Chronometer, a powerful weather-controlling rain staff recovered from Lost Mesa, and a letter from Gavin describing himself as her friend and admirer, with the story's threads setting up the fourth volume.