Original Version

Once the ride begins, the first part is like a typical dark ride, embellished with effects including a swinging axe and various other spooky-themed audio-animatronics displays. Along the way, an animatronic Scooby-Doo will tell the rider which way the carriage will go next until it reaches a platform.

As the platform ascends vertically it tilts from side to side giving riders the illusion that they will fall out. As it rises a short conversation between Scooby-Doo and Daphne can be heard. Once the carriage has reached the top of the elevator, and the top of the show building, it drops backwards 7 metres (23 ft) towards to turntable which spins the carriage around before continuing along the roller coaster track. This is where the true wild mouse section of the roller coaster begins. This section features various smoke, lighting and laser effects^[2] as well as a giant spider previously used in the Harry Potter Movie Magic Experience and Halloween Family Fun Nights. It is also musically accompanied by U.S. punk band MXPX playing a cover of the Scooby-Doo theme song. The ride ends with a final animatronic Scooby showing riders the way out of the wild mouse section, followed by one very small drop to get to the exit platform.

Next Generation (2018 update)

Although the ride's rollercoaster track is unaltered and its ghost train elements are still present, the ride's storyline has been significantly changed, although it is still themed to the 2002 film. Scooby-Doo now no longer appears in the ride until the very end in the exit queue. However, his initial voice over and disembarkment audio remains in use.

The creatures from the movie have escaped their enclosures and are attacking the riders. After the ride exits the station, using projection mapping effects, the train is attacked by two of the monsters breaking down the right-side wall, but the train gets away in time. Following the usual Ghost Train section, Riders are greeted with the mirror scene which now uses more projection effects to display the two monsters attacking the vehicle.

The ride then passes by several voodoo statues before coming to the Platform lift. Daphne and Shaggy both spot and talk to Scrappy Doo who, as the lift rises, appears on screens surrounding the riders and changes into his own monster form, then roars at the riders. Shaggy then says his iconic quote from the battle with Scrappy, which is, "You're a bad puppy!", followed by the claw used in the first movie pulling out the Daemon Ritus from Scrappy's chest. The train then drops backwards to the turntable as before, however the turntable is now surrounded by a disco like box with mirrors and neon lights.

The traditional wild mouse section remains relatively unaltered, however, the vat carrying the souls from the movie now sits in the centre of the room.

As riders leave this section they are now greeted by two projection mapped screens on either side of the train, but as the disco skull on the ceiling shines, the creatures become afraid. The train then makes its final small drop, however this small section is now incorporated into the ride's storyline and a screen above it shows one of the creatures screaming in the "Tiki Doll Lounge". As riders disembark and pass through the lounge, Scooby-Doo is seen hiding in a hut saying "I'm scared!" This scene uses the same animatronic and audio previously used at the beginning of the ride.^[11] Riders exit through a gift shop to buy various articles of Scooby-Doo merchandise, as well as on-ride photos.