Mark befriends a boy whose family is vacationing on a houseboat in the river. While out on an adventure together a hurricane quickly comes in. They get the boy's mother from the houseboat and Ben leads them to the safety of a cave.
As Tom and Mark are watching a mother bear play with its cub the mother gets shot by a swamp hunter. Tom issues as citation to the hunter and takes the cub. Ben appears to be jealous of the cub and when the hunter's boy steals the cub Mark assumes Ben chased it off. They discover that the boy stole the cub because living in the swamp he had no friends or pets. In an on the spot judgement, Tom tells the boy that the terms of his probation are to take good care of the cub, and the boy's father goes along with it.
Ben and Mark stumble upon fish poachers and their illegal smokehouse. The men threaten to kill Ben if Mark tells his father. Later Ben wanders off and Mark follows him onto the poachers' boat; they hide but the boat takes off when they hear Tom's airboat approaching. When they start shooting at Tom, Mark and Ben come to his rescue and the poachers are arrested.
Mark befriends shoeless Jenny Maddox at school. However, when Tom drops her off at her father's dock in the airboat, he discovers that Jenny's father is the alligator poacher he has been looking for. Before he goes back to arrest him, Jenny's father saves Mark from an alligator. Tom thanks him for saving Mark but still has to run him in, although he offers to help him in any way he can.
Mark gets Tom to put a radio transmitter on Ben so he can hear what he's doing when he's away. After Ben wanders off a plane carrying exotic animals crashes in the bush. Ben runs across the plane and when Mark hears the moans of the co-pilot, he figures out where he is and goes to help him. Finding the plane and the injured pilot and co-pilot, Mark calls in the location with Ben's radio. One of the animals is a tiger, whose cage has broken open- Ben protects Mark and the co-pilot. Tom and Ellen then arrive in the jeep and tranquilize the tiger.
Mark is mocked at school and on the school boat when he is the only child in his class that didn't bring in an Indian artifact for show and tell. He decides to go to the private island of Willie Sam Gopher to find his Seminole artifact. Mark befriends Willie's son Jimmie Boy, who wants to go to school so he and Mark sneak off the island. The next day Mark introduces Jimmie Boy as his 'artifact'. Willie comes into the classroom and grabs Mark but is scared off by Ben. Ultimately Willie agrees to allow Jimmie Boy to attend the school.
Ben gets restless when wild bears come near the Wedloe home during mating season. Tom explains to Mark Ben's natural instincts and Mark agrees Ben should be allowed to wander off to have a family. Missing Ben has left Mark sick and unable to eat but he returns to normal when Ben returns.
Developer Philip Garrett wants to clear cut and burn the brush to build a housing development on 60 acres of land adjacent to the game reserve. Concerned about all the animals that will die in the fire, Mark and Boomhauer hatch a scheme to get Mr. Garrett to the woods to see the animals and hopefully decide not to raze the land. They 'borrow' Garrett's wife's dog Hollyhock and tell him the dog liked it there when Mark walked him there and probably returned. But the dog escapes from Boomhauer's buggy and when they find it it is being pursued by wild bear Gertrude, protecting her three cubs (Eeny, Meeny, and Miney). Tom rescues Hollyhock and Mr. Garrett decides to leave most of the land as it is and just use a small area for cattle.
Professor Hugo brings his performing bear Victor to the Wedloe home. He has bought a bungalow in a retirement community and wants to release Victor into the wild. Hugo is unable to adapt to the wild, loses a lot of weight and makes enemies with the native wildlife. Tom and Ellen visit Hugo at his home and discover that he is lonely without Victor. The two are reunited and Victor is placed in a zoo and Hugo is made his zookeeper.
Mark leads some thieves to Boomhauer's honey farm and overhears them saying they will kill the game warden if he catches on. They notice Mark has heard them and tell him that if he says anything to his father they will shoot Tom. When the hives get damaged Ben is blamed but Mark doesn't want to say anything so that he can protect his father. When it comes down to Ben being punished, Mark tells his father what is going on. After a fight and Ben's intervention the thieves are apprehended.
A little girl gets lost in the Everglades. There is also an injured wildcat roaming the same area. Against his father's orders, Mark and Ben join in the search. Just as the girl is cornered by the wildcat, Mark and Ben find her and Ben scares the wildcat off. The main search party hears the commotion and the girl is reunited with her father.
A couple of con artists try to steal Ben to gamble on him in fights against dogs. Unable to get Ben, they find another bear. Tom and Ben break up the illegal bear-baiting ring.
A group of Seminole children approach Mark for help in attending his school, having been impressed by him getting Jimmie Boy into the school in the earlier episode ""The Invasion of Willie Sam Gopher"". Their main drawback is that they live on islands and don't have a boat to get them to school. Mark offers the winnings of the air boat race his father is in the next day to buy the boat. On the way to the race, Ellen tips the jeep and is trapped. Mark uses Ben to get the jeep off of her leg but she still can't move because it's broken. Mark contacts his father on the radio- he has just won the race and comes to help. At the victory celebration Tom gives the check to the Seminole kids to buy a boat and Mark gives Tom's winner's medal to Ben, who was the real hero of the day.
Tom offers Packy Benner some work, but he decides he can make more money more easily by stealing Ben and waiting for a reward. Tom is on to him and runs into Packy at the general store. Speaking so as to be overheard by Packy, he tells the shopkeeper that he's glad Ben is gone because he eats so much. Realizing that his scheme isn't going to work he returns the bear to Tom. Tom tells him that if he wants to give the bear back he wants money from Packy, tricking Packy into doing the work Tom previously offered for pay as compensation for taking Ben from him.
While on a shopping trip, Ben climbs into a delivery truck and gets separated from the Mark and Ellen. Subsequently Ben has a number of solo adventures including licking the shaving cream off of a man's face in a barber shop, ending up at a garbage dump after looking for food in a dumpster, and jumping off a railway bridge as a train heads towards him. Part one of two.
An injured Ben wanders into the camp of a couple of old carneys whose own bear is too old to perform anymore. They are going to keep Ben and train him but an announcement on the radio encourages them to return him to Mark.
Poachers are stealing the animals from a newly repopulated island. As they try to get away with their live cargo they also load Ben onto the truck, but he is spotted by Mark. The poachers are apprehended after a chase involving Tom, Boomhauer on his 'buggy', and the sheriff.
Mark and Tom have a surprise for Ellen's birthday. They are going to a cabin deep in the woods to spend a few days. When they get there they discover that the cabin has been broken into and is inhabited by a family of panthers. After they have scared off the panthers and regained control of the cabin, Ellen says this excursion is the dumbest idea Tom ever had and the best birthday of her life.
Hunting guide Joe Cardigan takes rich Miami big game hunter John Coberly into the swamp looking for a bear. Messing up on his first attempt and enticed by the promise of $1000 for a big bear, Cardigan steals Ben when nobody is home at the Wedloe residence. Tom, Mark, Boomhauer and his dogs track Ben's scent to Cardigan's cabin and force him to reveal where Ben is. Meanwhile, Coberly has spotted Ben but gets trapped under a log while tracking him.They find Ben and Coberly and Ben is able to free Coberly.
Mark takes Ben to Mama Jolie, a woman with alleged magical powers, to seek a remedy for Ben's lack of appetite. Ultimately, Mark and Tom help her son Geoffrey who is in the country illegally- they stop him from running and hiding and put him in touch with Immigration authorities.
St. Louis Carndinals star pitcher Bob Gibson is vacationing in the Everglades. When his small boat capsizes, Tom comes along in the airboat and gets him out of the water. Gibson agrees to give Mark some pointers and umpire his next game but is not impressed by the way Mark stretches the rules to gain an unsportsmanlike advantage. When Mark has a chance to strike out a batter who has dust in his eye, he decides to play fair and let's the batter compose himself.
Mark befriends an older boy with a minibike, Steve, and ignores Ben, who stops eating. Mark punishes Ben for being a nuisance and Ben runs away. Mark realizes that Ben is his only true friend when his Steve dumps him for an older boy with a Honda 90 motorcycle. Mark falls into a pit dug by illegal trappers while looking for Ben. When Mark is threatened by a cougar Ben comes to the rescue.
Looking for an injured deer they saw the day before, Mark and Ben hitch a ride directly into the area which becomes engulfed in a wildfire. The instinctively go to the river to seek refuge from the fire and Tom rescues them in the airboat.
Feeling neglected by his hard-working father, Mark's friend Jamie runs away from home. He hides in a shipwreck but it is in danger of being washed out to sea in a fierce storm. Based on a hunch, Mark leads everybody to the boat and they rescue Jamie.
Two armed criminals run into the swamp to elude the police after robbing a jewellery store. Tom, Mark and Ben are camping in the same area. While Mark and Ben are elsewhere, the fugitives force Tom to take them to another part of the swamp in his airboat to help their escape. Tom gets away from them and while they search for him, he overpowers one of them and Ben the other.
Right after Mark has been teased by girls on the school boat, his cousin Virginia comes to stay with the Wedloes for the weekend. Mark tries to entertain her but she is reluctant to do anything. Mark and Virginia find an old sea mine in the channel while fishing and she won't help him move it so he goes to his father for help. Virginia talks to Ellen about being afraid, and Virginia decides to face her fears by taking Ben and some rope to move the mine. When Tom hears of this, he, Mark and Boomhauer race to stop her. They get her and Ben to safety just as the mine explodes.
Tom's boss visits and offers him the job of District Manager, which means more money, no danger, and a move to the big city. The family visits the city and are impressed by the parks, schools, office, and culture. However they are less impressed by the unfriendly people, bad traffic and rude drivers. They also would have to get rid of Ben. When they get back home they decide that they like it just where they are.
Farmer Lloyd Larkin thinks local alligator Ol' Joe has turned rogue and is eating his pigs and chickens. Tom offers to catch him and move him away, enlisting the help of champion alligator wrestler Boomhauer. Mark and Ellen go fishing and discover that the pigs and chickens are actually being stolen by Larkin's farmhands. Tom captures them after a long chase and Larkin realizes Ol' Joe is harmless, and states that now ""Ol' Joe's gotta stay.""
A dolphin comes up the channel and hangs around the Wedloe's dock. He and Ben become friends and Mark considers him his pet. Mark is disappointed when he finds out that the dolphin escaped from Miami Seaquarium and has to go back before he is lured by the wild dolphins at sea in mating season. The lure of mating season is too strong for the dolphin, Marco Polo, and he heads to sea with Ben following.
Mark is despondent as he has not just lost his new pet, Marco Polo, but his old pet Ben. Frank from Seaquarium takes Mark and Tom out on a boat to find Ben and Marco Polo. They spot Ben on a small island and as they get his attention and he swims for the boat he is threatened by a shark. Marco Polo comes to the rescue and nudges the shark away from Ben. Ben climbs a ladder to get onto the boat, and Marco Polo is returned to Seaquarium.
After Mark has a series of mishaps that soil three pairs of Tom's pants, Tom is angry at him. Feeling unwanted, Mark moves in to Ben's shed. While fishing, a fisherman comes by the river and hires Mark as his guide. The small boat overturns at a rough spot in the river and Mark and Mr. Carter are threatened by alligators and a cougar. Tom hears the commotion and scares off the alligators while Ben scares off the cougar. Mark and Tom have a heart-to-heart conversation and clear the air between them.