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Before leaving work one afternoon, Billy Coleman spots a Redbone Coonhound in a fight with neighborhood dogs. He chases the other dogs away and helps it recover from its wounds. When it is feeling stronger again, he realizes he must set it free, knowing that it will find its way home. This event makes him revisit his past, and the two Redbone Coonhounds he had taken care of when he was a boy in the Ozarks.
Growing up in the Ozarks with his parents and three younger sisters, Billy Coleman, at age 10, wants to own a pair of Redbone Coonhounds but his parents tell him that they can't afford them. One day he finds an article in a sportsman magazine offering a pair in Kentucky for $25 each. He decides to earn the money himself. For two years, he works many different jobs, and manages to save $50. His grandfather writes to the kennel and finds out that the dogs have dropped in price by $5 each. He sends for two Redbone Coonhound puppies.
The mail does not deliver packages, and so the puppies have to be sent to the depot at Tahlequah, Oklahoma. Billy travels on his own by walking there and gets them. With the extra $10 his grandfather gave him, he buys gifts for his family: a pair of overalls for his dad, cloth for making dresses for his mom and sisters, and a bag of candy for his sisters. On the way back home, he spends the night in Robber's Cave on Sparrow Hawk Mountain. There he builds a fire and plays with the puppies. While trying to sleep, he hears a noise that at first seems like a woman screaming, but he soon realizes it is really that of a mountain lion from far away. Both puppies run to the mouth of the cave and challenge the cat. Billy worries for them, and he remembers that his father told him "mountain lions are scared of fire," so he makes fire and waits for morning. In the morning, he continues on. He comes to a sycamore tree and sees the names Dan and Ann carved inside a heart in the bark and decides to name the puppies Old Dan and Little Ann.
To train his dogs, Billy catches a raccoon with the help of his grandfather and uses the fur to teach them how to trail one. During their training, their personalities become apparent: Old Dan is brave and strong, while Little Ann is very intelligent. Both are very loyal to each other and to Billy. Old Dan has the brawn, and Little Ann has the brains.
On the first day of the hunting season, Billy takes his dogs out for their very first hunt. He promises them that if they tree a raccoon, he will do the rest. They are very ready to chase their first raccoon in a large tree, which Billy had before nicknamed "the Big Tree", and is one of the largest in the woods. As he tries to call his well-trained dogs off the hunt, they look at him sadly and he cuts down the enormous tree to keep his promise — an exhausting effort that takes him a few days of chopping and costs him blistered hands. In the end, when about to give up his effort, he offers a short prayer for strength to continue. Mysteriously, a strong wind starts to blow and the tree comes crashing down. Old Dan and Little Ann take the raccoon down.
Billy, Old Dan, and Little Ann go out hunting almost every night. As months go by, he brings more fur to his grandfather's store than any other hunter, and the stories of his dogs spread throughout the Ozarks. One day, he and his grandfather make a bet with Rubin and Rainie Pritchard, that his hounds can catch the legendary "ghost coon." The Pritchard boys set out with him to see if Old Dan and Little Ann can catch it. It leads them on a long, complicated chase, and the Pritchard boys want to give up. But Billy is determined. Finally, when they have it treed, Billy refuses to kill it. Just as Rubin starts to beat up Billy, Old Dan and Little Ann begin to attack the Pritchards' dog, Old Blue. Rubin runs to attack them with an axe, but he falls on it and kills himself. Billy is very distraught afterward. Finally he goes to Rubin's grave with some flowers, then feels much better.
A few weeks later, Billy's grandfather enters him into a championship raccoon hunt, putting him against experienced hunters and the finest dogs in all the country. Before it starts, he enters Little Ann into a contest for the best-looking dog, where she wins and is given the silver cup. On the fourth night of the hunt, Old Dan and Little Ann chase three raccoons, making it to the final round. The sixth night, they chase one before a blizzard hits. Billy, his dad, grandfather, and the judge lose sight of them. When they finally find them, Billy's grandfather falls and sprains his ankle which prevents him from walking. They built a fire, and when Billy's dad chops down a tree, three raccoons rise. The dogs take down two of them, and chase the third one to another tree. In the morning, the hunters find them covered with ice circling the bottom of a tree. The last raccoon wins them the championship and the gold cup.
Billy's mom and sisters are overjoyed. Billy keeps up his hunting. One night, however, his dogs tree a mountain lion. Old Dan howls defiantly, and the big cat attacks. Billy is horrified, and with his axe he enters the fray, hoping to save his dogs, but they end up having to save him. Eventually, the dogs defeat the mountain lion, but Old Dan is badly wounded, and Billy soon finds Old Dan's intestines in a bush. He dies the next day. Billy is heartbroken, and Little Ann is so sad that she loses her will to live, and dies a few days later on Old Dan's grave. Billy's papa tries to tell him that it is all for the best, because with the money he has earned, they hope to move to town. He does not completely recover until on the day of the move; he goes to visit the dogs' graves and finds a giant red fern between them. According to Indian legend, only an angel can plant a red fern. He and his family look at it in awe, and he feels ready to leave for town.