In Dapplewood Forest, three young animal “Furlings”—Abigail the mouse, Russell the hedgehog, and Edgar the mole—rush off to their daily school lesson with Cornelius the elderly badger. Cornelius shows his pupils a scale model of his flying device, which he calls a “Flapper Wingamathing.” When he releases the contraption into the air, the Furlings clamor to catch it, but accidentally crush it under a fallen book. After chastising the Furlings for their rowdiness, Cornelius takes them and his niece, Michelle, on a botany lesson, during which the Furlings frolic onto a paved road, narrowly evading an oncoming car. They inquire about the “monstrous” device, but Cornelius urges them to forget what they have seen. Later, a truck carrying a tanker of poisonous gas bursts a tire and crashes. The gases permeate through the forest, killing plants and driving most of the wildlife away. Upon returning from their excursion, the Furlings realize something is amiss and Michelle rushes home to find her parents dead at the kitchen table. Brief exposure to the gas knocks her unconscious, forcing Abigail to run inside and save her. Cornelius takes the children back to his house and tells the story of how his parents were killed by human exterminators. Estimating that Michelle has only two days to live, the elderly badger sends the Furlings to find herbal remedies for her damaged eyes and lungs. The first night of their journey, Abigail is captured by a hawk while running across an open field. Although she escapes the bird’s nest and rejoins her friends, the hawk chases them under a log at the edge of the clearing. Now lost, the boys blame Abigail for getting them into trouble, but the young mouse reminds her friends that they possess resourceful qualities that will help them find their way. The next morning, they encounter a flock of birds mourning the death of one of their own by a monster known as the “Yellow Dragon.” Edgar frees a baby bird stuck in the mud, and the townspeople rejoice. The group’s preacher directs the travelers toward a meadow, but warns them to beware the Yellow Dragons. As the Furlings cross the dusty field, they find themselves in the midst of a construction site ravaged by yellow excavators. After falling through a grate into a sewer, they are flushed out to a pond on the edge of a beautiful, flourishing meadow. There, a community of squirrels accuse them of coming to steal their food, but Edgar summons the courage to stand up to them. Ignoring the squirrels’ taunts, they attempt to collect one of the herbs, which grows on a steep cliff high above their reach. The Furlings build a full-size prototype of Cornelius’s Flapper Wingamathing that propels them into the air. Moments before Abigail can grab the herb, however, a gust of wind knocks her free and she dangles perilously from the flying machine’s wing. Edgar pulls her back onboard and realizes that a cluster of the plant has been caught between the wing flaps. As they fly home, they encounter a rainstorm and crash into a telephone wire, which singes the aircraft. The Wingamathing plummets to the ground and crashes in the familiar foliage of Dapplewood. Recognizing their surroundings, they run to Cornelius’s house with the antidote. Just then, humans surround the dwelling and Cornelius fears they are about to be exterminated. As he and the Furlings flee, Edgar trips, loses his glasses, and wanders into a trap. One of the humans, however, lets Edgar go and destroys the trap before continuing on his way. Relieved, Cornelius coats Michelle’s eyes with the herbs and says they must wait until morning to see if the remedy has worked. At daybreak, Michelle revives and Cornelius proudly admires the remnants of the Flapper Wingamathing the youngsters built. Moments later, Edgar, Russell, and Abigail’s families return to reunite with their lost children. Although the outskirts of the forest have been damaged by the gas, Cornelius says that if the animals work as hard as they did to save Michelle, it may be possible to restore their home to its former state.