In the El Malpais wilderness of New Mexico, Juniper Window lives in a cave in a deep collapse that his father has built into a home. They live a strange existence where the witch of the El Malpais stands in large Ponderosa pine trees on nights of the full moon and haunts a stark landscape of lava flows, cinder cones, caldera sunk into the earth, lava tube caves, and sandstone bluffs.

One night, after a depressing day at school, Juniper confronts the beautiful witch in her tree, and she chases him until he finally escapes down a lava tube that branches into other lava tubes deep in the earth. He finally reaches a great cavern with an underground river. There he sees "great lizards moving in darkness. Tongues flickered in and out of huge mouths with rows of razor-sharp teeth." When the largest of the lizards notices him, Juniper hears a voice in his head that tells him to follow to where a lava tube leads to the surface. Juniper is hesitant, but what other choice does he have? He could never follow the maze of tubes he'd scrambled down before he found the great cavern.

When, poised above the cavern in front of the lava tube he has been led to, he speaks out loud to the great lizard, the lizard informs him that it not a lizard but a dragon.

Thus starts an adventure that is partly a love story, partly a tale of madness in a world filled with the violence and problems confronting contemporary society, including drug use, and partly a story of healing, family, and redemption. Poetic prose sings as events sweep over the wild landscape of the El Malpais and Ramah, New Mexico and dragons and human hurtle toward a climax that promises enormous changes in a world that has no idea of what is about to happen.

As the powerful adventure continues, the dragons discover their heritage as great dragons who have been driven to the cavern beneath El Malpais to avoid extinction, Lily, a Navajo girl that Juniper falls in love with, finds a way to heal her Grandfather of his alcoholism, and Juniper, his father, and his mother at last put the past behind them on a hill beside Four Windows Caves as the dark sky on a Christmas night is filled with the flight of dragons.

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