* The fact that Eric would create a video game based on his friends and their various adventures is pretty heartwarming.
* Daphne comforting a frightened Scooby over the discussion about the Phantom Virus.
* The pride Kaufman shows in his students' invention. Eric offers him a share of the prize money they are likely to win for the laser, saying he helped a lot too, but Kaufmann replies that nourishing young minds is its own reward for him.
* Shaggy and his cyber counterpart quickly bond over eating and graciously give some of their food to Scooby, only for him to distract them so Cyber Scooby can steal it. Still, the Scoobies sharing the food is pretty cute.
* ''[[LovableCoward Scooby]]'' climbs up a mountain with lava oozing down its side to help a mama pterodactyl save her trapped baby. The baby [[AndroclesLion returns the favor and takes Scooby to safety right before the lava reaches the nest.]]
** Note that Scooby ''didn't'' know that the box of Scooby Snax needed to pass the level were in the pterodactyl nest. Scooby climbed an erupting volcano to rescue a baby pterodactyl ''entirely'' out of the goodness of his heart!
* The cyber gang talk about [[DoAndroidsDream how much they like it in the tenth level and how they can finally live peacefully]] due to how all of the monsters stay at the theme park, guarding the Scooby snacks.
* After sneaking into danger to help out, Cyber Scooby bites at some wires that Fred is tied up in to try and free him.
* After beating the final level, Scooby shares the Scooby snacks with his alternate counterpart.
* Daphne [[Main/SmoochOfVictory kissing]] Fred for bullfighting a ''lion'' and not getting her jacket damaged.
* The two Mystery Inc. teams, real and virtual's goodbye to each other.
* Just after Scooby and the gang get sucked into the virtual world, Officer Wimbly, the campus security guard who's been kind of a jerk to them since the moment he first met them, seems genuinely concerned for their safety and was the first to ask Eric and the others if there was anything that could be done to get them out of the game.