Scooby-Doo! and Krypto, Too!

Months have passed since the Justice League disappeared, and Lois Lane and Jimmy Olsen begin probing the Hall of Justice for clues. Their investigation is interrupted when a menacing phantom appears and pursues them through the halls. Realizing they need help, they decide to bring in Mystery Inc.

On the way to Metropolis, Mystery Inc. learns the city has fallen under the control of various villains in the League's absence. Giganta, Solomon Grundy, the Joker, Harley Quinn, General Zod, Non, Ursa, and Brainiac roam freely, sowing chaos. The gang steels themselves for a difficult mission ahead.

The team barely escapes to the Daily Planet and reunites with Lois Lane and Jimmy Olsen. They explain the disappearance of the Justice League and the resulting villain takeover, outlining their plan to investigate further. They resolve to coordinate with allies to find answers.

During a tour of the Hall of Justice, the group encounters Lex Luthor, Mercy Graves, and Rex Ruthor, Luthor's robot dog. The phantom threat tests the hall's defenses, raising tensions. The encounter sets the stage for uncovering the mastermind behind the crisis.

A phantom suddenly materializes and menaces the group inside the Hall of Justice. Krypto, Superman's dog, leaps to the rescue and uses his powers to drive back the phantom, triggering a lockdown to prevent its escape.

Trapped with Luthor and his allies by the lockdown, the gang negotiates their situation. Krypto introduces Scooby-Doo to the team, and the two dogs quickly form a bond.

Shaggy, Scooby, and Krypto raid the Kitchen, accidentally summoning holograms of the Legion of Doom. The holograms cause chaos until Krypto shuts them down, revealing holographic footage of the moment the Justice League disappeared.

The gang discovers holographic footage showing the moment the Justice League disappeared. Solomon Grundy infiltrates the building, initiating a long chase with Mystery Inc. and their allies.

Velma uncovers that Mercy Graves orchestrated the phantom hauntings to convert the Hall of Justice into her own headquarters. She planned to trap the Justice League in the Phantom Zone using a Phantom Zone Projector.

Before the mystery can be solved, Lex Luthor hijacks Mercy's scheme and reveals his own plan to rule Metropolis with a robot army. Rex is revealed to be a robot and engages in a clash with Krypto over the Phantom Zone Projector.

Krypto defeats Rex and uses the projector to trap the robot army, freeing the Justice League and even Solomon Grundy. The Phantom Zone is released from the threat, and the heroes are liberated.

Luthor and Mercy are arrested, and Grundy’s aggressive friendship attempts with Scooby are exposed. Mystery Inc. meets Clark Kent, who Velma recognizes as Superman, and Jimmy ends his relationship with Daphne. Scooby and Krypto share a final snack with The Flash.