Scooby-Doo! and Krypto, Too!

Mercy Graves orchestrated the phantom hauntings to convert the Hall of Justice into her own supervillain headquarters. She used a Phantom Zone Projector to trap the Justice League in the Phantom Zone, removing the heroes from the equation so she could take over the building without opposition.

Earlier in the film, the phantoms that attacked Lois and Jimmy were revealed to be part of Mercy's scheme to clear the Hall of Justice of its defenders.

Lex Luthor was already aware of Mercy's phantom scheme and waited for the right moment to seize control. When Mercy's plan was underway, Luthor revealed he had been monitoring the situation and used the chaos to mask his own ambition: ruling Metropolis with an army of robots. He turned Mercy's Phantom Zone Projector toward his own goals.

Lex Luthor's presence during the Hall of Justice tour, alongside his robot dog Rex Ruthor, hinted at his deeper involvement in the crisis.

Solomon Grundy's true motive was surprisingly wholesome, he was trying to befriend Scooby-Doo. His aggressive and clumsy behavior throughout the film, including infiltrating the Hall of Justice, was his awkward way of attempting to make friends with the Great Dane. He was never genuinely malicious.

Grundy's aggressive interactions with Scooby during the chase scenes were actually attempts at friendly engagement, not hostile attacks.

Krypto defeated Rex Ruthor (the robot dog) in combat and seized control of the Phantom Zone Projector. He then used the projector to trap Luthor's robot army and reverse the process, freeing Superman, Wonder Woman, Aquaman, the Flash, Hawkman, and even Solomon Grundy from the Phantom Zone.

Krypto's superpowers and determination to help his owner Superman drove his victory over the mechanically-enhanced Rex.

Velma Dinkley deduced that Clark Kent was Superman upon meeting him after the crisis was resolved. Her sharp detective instincts allowed her to connect the clues, recognizing Clark's presence, the timing of events, and the fact that Superman disappeared when Clark appeared.

Velma's reputation as the team's master detective foreshadowed her ability to uncover the superhero's secret identity.

Rex Ruthor was revealed to be a robot created by Lex Luthor. He served as Luthor's loyal enforcer and was equipped with Kryptonite in his circuitry specifically to counter Krypto's powers. Rex clashed with Krypto over control of the Phantom Zone Projector before being defeated.

Rex Ruthor's introduction as Luthor's dog hinted at his true robotic nature and his purpose in the larger scheme.

The phantoms were created by Mercy Graves as part of her scheme to take over the Hall of Justice. She used the Phantom Zone Projector to project spectral threats that would drive people away from the building, making it easier for her to establish her supervillain headquarters without interference.

The initial phantom attack on Lois and Jimmy set the mystery in motion and established the supernatural threat at the Hall of Justice.

Jimmy and Daphne amicably ended their brief relationship at the film's conclusion. The breakup was portrayed as a mutual, friendly decision rather than a dramatic split, with Jimmy acknowledging they wanted different things as they returned to their respective lives.

Jimmy's cheeky proclamation of Daphne as his girlfriend earlier in the film established their relationship, making its amicable end a minor but honest character moment.

The Justice League was trapped in the Phantom Zone by Mercy Graves using her Phantom Zone Projector. Holographic footage uncovered by Shaggy, Scooby, and Krypto revealed the exact moment of their disappearance, showing Solomon Grundy infiltrating the Hall of Justice as part of Mercy's coordinated scheme.

The mysterious disappearance of Earth's greatest heroes set the entire plot in motion and explained the power vacuum that allowed villains to overrun Metropolis.