The Indigo Spell follows Sydney Sage, a young Alchemist, a member of a secret human society that keeps the existence of vampires hidden from the world, as she navigates dangerous supernatural threats and a forbidden romance.
Sydney's history teacher, Ms. Terwilliger, who is secretly training her in human magic, wakes her at three in the morning to cast a scrying spell in the desert. Using a mirror and moonlight, Sydney enters a trance and sees a dark red Victorian house near Los Angeles. Ms. Terwilliger is alarmed and tells Sydney she must rapidly improve her magical skills for her own protection but refuses to explain why.
Sydney flies to Pennsylvania for the wedding of Sonya Karp and Mikhail Tanner, two vampire-world allies whose marriage is meant to improve relations between the Alchemists and the Moroi, a race of living, non-violent vampires. Her flight is overbooked, and she ends up seated beside Adrian Ivashkov, a Moroi who recently confessed his love for her. She rejected him because Alchemist doctrine forbids human-vampire relationships. Adrian tells her he is done sulking but not done loving her, and his calm certainty unsettles her.
At the reception, Adrian publicly asks Sydney to dance, a shocking breach of etiquette between their races. While dancing, he suggests she use the scrying spell to locate Marcus Finch, a mysterious ex-Alchemist Sydney has been trying to find. That night she performs the spell in a snowy field, and Adrian identifies a building in her vision as the Old Mission Santa Barbara, giving them Marcus's location.
Back in Palm Springs, Ms. Terwilliger reveals the full truth. Her older sister Veronica maintains her youth by stealing it from young women through a dark spell, leaving victims comatose and prematurely aged. Sydney, as an untrained magic user with significant natural power, is a prime target. Ms. Terwilliger gives her a garnet necklace to mask her ability and asks Sydney to help hunt Veronica, since investigating directly would alert her sister. Sydney reluctantly agrees.
Sydney drives to Santa Barbara, breaks into Marcus's apartment, and is attacked by him. She fights him off with self-defense skills and a chemical irritant. Marcus reveals he has been looking for her. He leads a small underground group of ex-Alchemists and defectors from the Warriors of Light, a human anti-Moroi extremist group. He claims the Alchemist tattoo can impose compulsion beyond preventing discussion of vampire affairs. Sydney brings Marcus to Adrian for healing. Adrian, seeing the bruise on Sydney's face, punches Marcus before learning the injury was accidental. He heals them both with spirit, a rare form of Moroi magic.
Sydney and Adrian investigate Veronica's whereabouts and warn potential victims. Disguised with a wig and spirit magic, they visit the bed-and-breakfast from Sydney's vision, where the receptionist Alicia confirms Veronica recently stayed but has already checked out. When Alicia later reports Veronica's return, they rush back but find the room hastily abandoned. During this visit, Sydney's cross necklace breaks and is left behind. On a separate trip, they arrive too late to warn Lynne Titus, a college student found comatose and prematurely aged. Sydney blames herself, partly because she and Adrian were kissing at a nearby party instead of searching.
Marcus asks Sydney to infiltrate the Alchemist facility in St. Louis and steal surveillance footage proving that Master Jameson, a high-ranking Warriors of Light official, visited the facility. A spy overheard Jameson discussing a search for a "missing girl" who could cause problems for the Moroi. Sydney and Eddie Castile recognize this may refer to Jill Dragomir, the Moroi princess they are hiding in Palm Springs. Eddie is Jill's bodyguard and a dhampir, a member of the warrior race that guards Moroi.
Sydney travels to St. Louis under the pretext of attending Alchemist holiday services, where she encounters her father and her younger sister Zoe. Using Ian Jansen, a fellow Alchemist with a crush on her, Sydney gains access to the facility's secure levels. She casts an invisibility spell, creates a fireball to sabotage a computer as a distraction, and copies surveillance footage onto a thumb drive. The video shows Master Jameson at the checkpoint alongside a senior Alchemist director, confirming the conspiracy.
Ms. Terwilliger intensifies Sydney's combat training, teaching her to summon fireballs. She also gives Sydney a spell that produces a callistana, a small crystalline dragon that warns of dark magic. The callistana bonds with both Sydney and Adrian, who name it Hopper. Adrian begins visiting Sydney nightly through spirit dreams to protect her from magical attacks, and they grow closer.
Sydney shows the stolen footage to Marcus. He injects charmed silver liquid into her tattoo to break its compulsion, but Sydney refuses to go further. She will not seal the tattoo in Mexico or leave the Alchemists, arguing she can accomplish more from within. She recognizes that Marcus's group uncovers information without ever acting on it.
The romantic tension reaches a breaking point in a spirit dream where Sydney initiates a passionate encounter. Jill, who experiences Adrian's emotions through a psychic bond created when he used spirit to bring her back from the dead, accidentally witnesses everything. Sydney is mortified. Overwhelmed by fear of discovery and her growing feelings for Adrian, she tells him she is leaving for Mexico with Marcus. Adrian argues she is running from her feelings, not from danger. Sydney walks out.
Sydney's car is then destroyed by a foam-like substance, and she finds her lost gold cross in the wreckage, burning with magical residue. She realizes someone used the cross to track her. Ms. Terwilliger gives her a new protective charm, and Sydney recognizes it as identical to a necklace worn by Alicia, the bed-and-breakfast receptionist. The truth crashes down: Alicia is not Veronica's employee but the true predator.
Sydney and Adrian rush to Ms. Terwilliger's house and find Alicia inside. Alicia reveals she absorbed Veronica's power along with that of several other victims and has come for Ms. Terwilliger, who has been weakened by weeks of casting protective magic. Sydney uses ice and fire spells, and in a final act against her nonviolent nature, casts a transmutation spell to hurl razor-sharp metal at Alicia's face. Alicia falls into the burning basement. Adrian carries Sydney out. Ms. Terwilliger is found safe in a nearby park, having escaped earlier. No remains are found, suggesting Alicia survived.
On the day Sydney plans to leave for Mexico, Jill confronts her, insisting she is running from love, not danger. Sitting in Marcus's car at the train station, Sydney changes her mind. She drives to the Getty Villa in Malibu, following coordinates Adrian left in a note, and finds him by a reflecting pool. They kiss among the classical gardens, and Sydney acknowledges her feelings for the first time. They commit to a secret relationship.
When Sydney returns to her dorm at Amberwood Prep, her boarding school, she finds Zoe waiting, now bearing a golden lily tattoo, the Alchemist mark, on her cheek. Zoe has been assigned as a junior Alchemist apprentice. She is thrilled, but Sydney is horrified, realizing her sister's constant presence will make it nearly impossible to hide her romance with Adrian, her magical training, and her investigation into Alchemist secrets.