Months after the Justice League mysteriously vanished, Lois Lane and Jimmy Olsen dig into the strange happenings around the Hall of Justice, only to be chased off by a menacing phantom. Wasting no time, they call in Mystery Inc. for help, and the gang heads toward Metropolis with a sense of urgency, hoping to unravel a mystery that could threaten the whole city.
As they roll into town, Metropolis feels different—overrun by a frightening lineup of villains, including Giganta, Solomon Grundy, the Joker, Harley Quinn, General Zod, Non, Ursa, and Brainiac—an army loosed in the wake of the Justice League’s disappearance. The Mystery Inc. crew barely escapes to the Daily Planet, where they reconnect with Lois and Jimmy. Jimmy, in a moment of cheeky boldness, proclaims Daphne Blake as his girlfriend, much to Daphne’s exasperation, and the two groups begin to piece together what’s really going on. Together they tour the Hall of Justice and cross paths with Lex Luthor, Mercy Graves, and Luthor’s loyal canine Rex Ruthor, all of whom become key players in the unfolding drama.
Then the phantom reappears with terrifying force, only to be repelled by a mysterious, superpowered dog. This new ally locks down the building to keep the phantom from slipping away and introduces himself to the others as Krypto, Superman’s devoted pet, who quickly becomes fast friends with Scooby-Doo. The trio—Shaggy, Scooby, and Krypto—embark on a playful but perilous raid of the Kitchen, believing it to be a real one. A misstep triggers a cascade of holograms of the Legion of Doom, scrambling the control panel and plunging the hall into chaos. Shaggy and Scooby’s quick improvisation distracts the holograms long enough for Krypto to shut them down, and the trio uncover holographic footage that reveals the moment the Justice League disappeared and exposes Solomon Grundy’s infiltration of the building, setting off a high-stakes chase.
Solomon Grundy vanishes in a flash of light, but the trouble doesn’t end there—more phantoms appear in the Hall of Justice. Velma Dinkley steps up with a brilliant deduction: Mercy Graves is behind the whole scheme, intent on transforming the Hall of Justice into her own supervillain headquarters. She planned to trap the Justice League in the Phantom Zone using the Phantom Zone Projector, explaining the spectral threats haunting the building. Before the gang can declare victory, Lex Luthor hijacks Mercy’s plan, admitting he already knew about it and used the ruse to mask his own ambition to rule Metropolis with an army of robots. Rex Ruthor is revealed to be a robot, and he clashes with Krypto over the Phantom Zone Projector while the others hold off the growing robot army. Even with Kryptonite built into Rex’s circuitry, Krypto emerges victorious and uses the projector to trap the metal soldiers, freeing the Justice League—Superman, Wonder Woman, Aquaman, the Flash, and Hawkman—and Solomon Grundy in the process.
In the wake of the showdown, Luthor and Mercy are arrested, and Grundy’s surprising motive comes to light: he’d been trying to befriend Scooby, albeit in his own rough way. With the case closed, Mystery Inc. meets Clark Kent, who Velma immediately recognizes as Superman, and a bittersweet moment arises when Jimmy and Daphne amicably part ways. The film closes on a lighter note as Scooby-Doo and Krypto share one last snack together with the Flash, signaling a hopeful reunion of old friends and new allies in a city saved from a very strange threat.
