Slasher and Boof are first seen when they intrude in the FernGully rainforest and growl viciously at the baby animals that were under Crysta's care. Boss then cracks a whip at both dogs and commands them to attack, which they do. With the dogs' help, the poachers manage to capture a baby koala, a baby bandicoot, and a joey kangaroo named Nugget. Later, the captive Nugget manages to free himself and then frees the other baby animals. However, Slasher and Boof eventually notice and attack once again. In the ensuing chaos, a fire is accidentally started in the rainforest, and Slasher becomes separated from Boof. Later, Slasher is seen mourning over his friend, though Boss tells him not to and to focus on guarding the captive baby animals.
Sometime later, Crysta hears a howling noise and rushes over to find Boof with his front paw stuck in a hunter's trap. She attempts to free him, but is not strong enough to remove the trap from his foot. She then enlists Goanna's help, who is reluctant at first, but then complies by removing the trap from Boof's paw and then throwing the trap into the water. Crysta tends to Boof's wounded paw and when she asks if his paw feels better, he thanks Crysta by licking her affectionately. Goanna growls angrily at Boof who cowers, though Crysta assures Goanna that Boof is just being friendly. With Goanna's help, Crysta and Boof travel along the river on a log to where the dog's owner currently is.
Eventually, Boof and Crysta arrive at a dock where a ship is about to transport the captive baby animals. Boof is overjoyed to see his friend Slasher (who initially growled at Crysta when she approached him). Slasher is overjoyed as well to see his friend Boof, and the two dogs reunite with one another and lick each other affectionately. Boof and Slasher then turn on their cruel owners, but in doing so, Boss locks them away in a small room on the ship. However, the dogs manage to escape after attacking Mac, who had been chased into the room with them at one point by Pips and the Beetle Boys.
When the captive baby animals are rescued, Nugget is seen struggling to get out of his cage but falls in the water. Boof and Slasher immediately jump in to save him, but are unable to find him underwater. Boof and Slasher, along with Crysta and the gang, mourn over the loss of Nugget. However, Nugget gets their attention and shows that he's all right, causing Boof and Slasher to cheer by howling and barking joyfully. Boof and Slasher want to go back to Ferngully with Crysta, but she says that they belong in the human world. Boof and Slasher whimper sadly until Budgie (a human girl that Pips and the Beetle Boys encountered and befriended earlier) decides to adopt them. Happy to hear this, Boof and Slasher run over to Budgie and lick her face affectionately.
Boof and Slasher are last seen in Budgie's grandfather's car panting and smiling happily, as they now have a new home and a loving owner.