That night, Scooby-Doo and Shaggy sneak out of their room to search for the kitchen and are chased by the monster, accidentally destroying the playing field in the process. Locksley sees the carnage and, enraged by Scooby and Shaggy's claims of almost becoming Loch Ness Monster victims, orders Shannon to repair the damage, threatening to demote the highland games to a miniature golf tournament if she doesn't. Velma discovers, to her surprise, that the Loch Ness Monster tracks head into town instead of the loch. The next day, the gang and Shannon travel to Drumnadrochit, Inverness-shire. After enlisting the help of the Haggarts to rebuild the field, Fred, Daphne, Velma and Shannon take Professor Pembrooke's boat, filled up with out-of-date research equipment, to search for the Loch Ness Monster by sea, while Shaggy and Scooby take the Mystery Machine and search by land. While Shaggy is distracted, a hand switches a sign on the road leading to Shaggy getting lost. Both groups are attacked by the monster, which is seemingly in two places at once.
After returning the badly damaged boat back to Professor Pembrooke, the gang discovers Sir Ian has taken it upon himself to patrol the waters with a high-tech ship to prevent any further "peculiarities", as he's still not convinced of the monster's existence. On Locksley's ship, the gang and Shannon find something deep in the loch using sonar equipment. They take Locksley's minisub down to investigate. In the water, the gang is attacked by the Loch Ness Monster, but is saved by a large magnet claw on the ship (before reaching the surface, the Loch Ness Monster knocks the submarine's sonar camera off of its hull). When they return to Blake Castle, they find Del sleeping in the Mystery Machine, who explains his van has been stolen. The Loch Ness Monster later chases the gang, Shannon and Del into a bog, where it's revealed to simply be a canvas covering Chillman's van. Fred deduces it to be a decoy and sets up a trap to catch the real one.
Fred sends Shaggy and Scooby out on the loch to act as bait, while he and Del prepare to use nets to surround the cove to capture the Loch Ness Monster. A large fog appears, blocking visual contact with Shaggy and Scooby. Making matters worse, Locksley's crew mutinies because they want to capture and sell the Loch Ness Monster, and capture Daphne, Shannon, and Locksley himself. The Loch Ness Monster attacks Shaggy and Scooby, chasing them out of the cove. Locksley's ship attaches to the nets, dragging Del and Fred with it. The crew attempts to harpoon the Loch Ness Monster, but Daphne and Shannon distract them long enough to make them miss. Just as the Loch Ness Monster is about to attack Del, Fred, and Locksley, Daphne captures it by using the ship's magnetic claw. All of a sudden, a second Loch Ness Monster appears and gives chase to Shaggy and Scooby but falls into a previously set trap. This monster is revealed to be a huge puppet controlled by the Haggart brothers, and the one Daphne captured is a home-made submarine operated by Professor Pembrooke. Pembrooke used a secret entrance in her boat to go into the monster sub and operate it. She also hired the Haggart brothers to man the second monster on the assumption that they wanted to sabotage the games, but Angus and Colin reveal that they just wanted to do it as a prank. Velma explains that Pembrooke's plan was to use her machine to convince Locksley the real monster existed and enlist his aide in finding it.
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