En route to Metropolis, the gang discover that the city is overrun by villains (Giganta, Solomon Grundy, Joker, Harley Quinn, General Zod, Non, Ursa, and Brainiac) as a result of the missing Justice League.

Continuing their investigation, Shaggy, Scooby, and Krypto raid the kitchen, but accidentally summon holograms of the Legion of Doom, malfunctioning the control panel.

Before the gang can declare the mystery solved, Luthor suddenly hijacks Mercy's scheme, revealing that he knew about it and used it to cover up his plan to rule Metropolis with an army of robots.

Despite Rex having the advantage with Kryptonite in his circuitry, Krypto eventually manages to come out victorious and uses the projector to trap the robot army and free the Justice League (Superman, Wonder Woman, Aquaman, Flash and Hawkman) and even Solomon Grundy.

With the case closed, Mystery Inc. meets Clark Kent, Jimmy "breaks up" with Daphne, and Scooby and Krypto share one last snack with Flash.