Happy Halloween, Scooby-Doo!

The Mystery Inc. gang slips into Crystal Cove to participate in Elvira's Halloween of Horrors Parade and capture the Haunted Scarecrow. They stage a covert operation among the crowd, hoping to trap the villain. The reveal identifies the Scarecrow as Dr. Jonathan Crane, a former Arkham escapee.

They unmask the Scarecrow as Dr. Jonathan Crane, and Velma explains how she traced a fan letter to Elvira and measured fear-gas leakage to piece together the plot. The crowd reacts as Crane's identity is revealed and the plan appears to succeed. The moment cements Crane as the mastermind behind the haunting.

Gas drones carrying fear gas fill the sky, triggering panic across the parade grounds. Scooby-Doo and Shaggy fend them off by launching Halloween candies as improvised projectiles. The crowd's fear reveals Crane's larger plan is still in motion.

Crane is pulled away by federal agents, claiming the drones did not leak, which hints that Velma may have missed a crucial detail. His cryptic remark suggests a deeper conspiracy behind the hauntings. Velma is left with a nagging doubt as Crane is taken away.

The chase results in severe damage to the Mystery Machine, leaving Fred despondent as the team realizes they may be stranded. The group must adapt to the loss as the threat grows. Fred's disappointment foreshadows upcoming twists.

Scooby and Shaggy discover a stray disabled drone in a pumpkin patch bearing 'Tot Alli Frame' and a truck full of toxic waste. Contact with Crane's fear formula turns pumpkins into animated monsters that chase them. They hurry back to town to warn the others about the 'Jackal Lanterns,' only to be dismissed and berated by Velma.

Fred and Velma meet Bill Nye, who gifts them a modernized vehicle called Mystery Machine X. Fred remains attached to the original, expressing reluctance to switch. The new ride becomes central to the gang's response to the escalating danger.

Jackal Lanterns pursue and abduct a female reporter, and the giant master monster consumes her to become another monster. The street chase follows, forcing the gang to split into three groups to pursue different angles. The town is thrown into chaos as the Jackal Lanterns close in.

The gang splits into three groups as the Jackal Lanterns close in: Mystery Machine X with Fred, Velma, and Bill Nye; Elvira with Daphne; and Scooby with Shaggy and Mike and Michelle. They encounter the Sheriff, who is gobbled up by the Giant Jackal Lantern riding the original Mystery Machine. Velma frees Dr. Crane from the federal truck, but Crane is consumed by the Giant Jackal Lantern, and the real Mystery Machine is destroyed.

The surviving members gather in Velma's mind palace to recount the night's events and piece the truth together. Velma takes a leap of faith, entering the Giant Jackal Lantern's mouth and emerging unharmed. She discovers the giant monster is a machine and that the others are safe inside, with drones revealed as the real threats.

Toe Omnitech head Cutler Toe is revealed as the mastermind, impersonating the Sheriff to frame the gang and target the lithium mine. Velma and Daphne trace a hologram of the Jackal Lanterns to locate Toe's car, aided by federal agents. The Scarecrow's vengeance prompts a final pursuit, but Toe vanishes and no trace of him remains.

With the case closed, the gang is invited to a roadside Halloween celebration, and Elvira delivers a monologue that breaks the fourth wall with a spooky reveal. The group, including Bill Nye, assists Fred in rebuilding the Mystery Machine and looks ahead to future adventures. The film closes on a festive note as the town returns to normal and the mischief ends.