Two leopard men take the Professor to the forgotten city of Opar, where Queen La is hoping for a king. She refuses the Professor and has the leopard men do what they wish with him. When Tarzan and the others find out, they all head for Opar, just in time to save the Professor. However, after seeing Tarzan, La falls in love with him and plans to get rid of Jane.

Two deserters of the French Foreign Legion called Hooft and Hugo flee into the jungles of Africa. Unfortunately, their former superior, Lt. Colonel Staquait, finds their tracks and vows to follow them to the ends of the earth. Tarzan rescues the deserters from the perils of the jungle and the duo begin taking advantage of the resulting hospitality. Jane, being suspicious of the parasitic pair and their fantastic stories, decides to turn them in, only to realize who the real criminal is.

Baruti and Jamila, an elephant couple, migrate into Tantor's herd to protect their hypochondriac son, Jabari, from the mad rampages of Mbaya, an elephant gone "rogue". Tantor and Jabari instantly bond, but through a series of coincidences, Tantor comes to believe that he's responsible for Mbaya's recent rampage through Tarzan's protectorate and retreats into the jungle. Meanwhile, Jane attempts to discover something that Tarzan's afraid of.

Tantor drinks water from the river and gets ill. Tarzan, Jane, and the Professor go upstream to find out what's poisoning the river while Terk tries to save Tantor. Along the way, they lose their boat and get captured by a group of natives who blame them for poisoning the river.

The Professor and Jane figure out that it's a mine that's poisoning the river and that Tarzan and the native warrior are in trouble. Tantor, Terk, Jane and the Professor come up with a plan and must work together with the natives to save Tarzan and get rid of the mine once and for all.

Tarzan and Terk find an injured gorilla named Gobu in the forest. Little do they know, but he is under orders from his leader to lure Tarzan back to Gobu's family. Once the injured gorilla (who Terk has taken a strong shine to) is better, he and Tarzan embark on the long journey to Gobu's home, only to find the evil Tublat, a bull ape who was expelled from Kerchak's family many years before, was waiting there to trap him. Meanwhile, Jane and the Professor attempt to teach Terk to be more lady-like.

The Professor eagerly awaits the arrival of a Doctor Doyle. Upon arrival, everyone is surprised to find that Doyle is actually a woman. Doctor Robin Doyle had come to Africa to study Keewazi's tribe with the Professor. While studying, they find some of the older men to have quite startling ages (from 500 to 700), and learn about a great fountain. The professor, who feels he's too old for Robin, secretly sets forth to find this fountain.

When the Professor's rival, Samuel T. Philander, visits Africa, he must come up with something spectacular to become famous on before Philander. That's when Tarzan tells them about Pellucidar, an underground world where dinosaurs live. However, Philander follows them there and takes pictures of the dinosaurs. The Professor, having no camera with him, attempts to best Philander by taking something else with him.

When Terk and Tantor accidentally spill some of the fluid from the giant flowers the Professor was studying onto a few beetles, it makes them giant themselves. To stay out of trouble, they keep it a secret. But how can you keep a couple of huge beetles a secret?

Tarzan and Jane return from a trip to the Waziri village to find the Professor missing and his camp in ruin. Jane momentarily fears the worst, but soldiers on with Tarzan in an attempt to determine her father's whereabouts and condition—a pursuit impeded by the hordes of apparently mad animals, including Terk and Tantor, destroying everything in their path and pleading for the cessation of a mysterious, unheard ringing.

Doctor Robin Doyle returns to the jungle with her nephew Ian, a bookish child with few friends who spends his time collecting butterflies. While Robin and the Professor spend some quality time "spooning", the task of entertaining Ian falls to Tarzan, whom Ian sees as a much-needed role model. Lacking any other experience, Tarzan fills the day with activities he enjoyed as a child, and it's not long before the boy has discarded his formal trappings for a loincloth. None of this sits quite well with Jane, who worries about the dangers of a small child swinging recklessly from tree to tree—and what the good doctor will say when she finds out.

The leopard men attack the treehouse and, rather than retrieving Tarzan (as the gang expects), make off with Jane, and gas the others. Once conscious, Tarzan, Tantor, Terk and the Professor set off for Opar to rescue her, only to find Queen La, staffless and at the mercy of a leopard, begging for help. Despite the Professor's warning, Tarzan intervenes and forges a temporary alliance with La to free his wife from La's rebelling minions. However, he is unaware of the true intentions of La and the leopard men.

The jungle is visited by the former President Teddy Roosevelt and, while on the hunt for animal specimens to study (which Tarzan heavily disapproves of), both are kidnapped by conspirators. In the process of escape, Tarzan teaches the President the importance of respecting nature, and he gains a new appreciation for it by the time he leaves, promising to bring that lesson home to America.

Disgusted by the decay near the elephant territory, Jane tries to use an English vine to cover up the scent. But the vines cover up everything and are too poisonous to eat. While Jane and the Professor try to think of a solution, Tarzan invites the elephants to live with the gorillas, but how long can they live together in harmony?

The Professor learns about a spiritual silver ape that, supposedly, cures the injured of the jungle. Not believing this is a spiritual creature, he plans to study it more. But when Philander steals his notes and finds out about the ape, he plans to capture it.

Tarzan's leadership of the gorilla family is challenged by a young silverback male named Moyo. Moyo wins leadership only when Tarzan sacrifices his in the fight in order to save Moyo's life. The new leader leaves with the gorillas to escape the threat of Histah, a giant python that used to terrorize the gorillas when Kala was young, leaving Tarzan to choose what's dearest to him—Jane or the gorillas.

A logger's daughter and workers fall ill with a dangerous disease. Tarzan seeks to obtain a cure for the disease, only to find out the cure may have been destroyed by their irresponsible logging.

A film crew arrives in the jungle to shoot an action movie. Tarzan, being unaware of this, interferes in the process, causing him to appear in the scenes unintentionally. The film's male lead actor becomes jealous after being replaced by Tarzan and attempts to destroy the footage, causing a huge fire at the trading post.

Terk gets scared when she sees a monster, which is later revealed to be a velociraptor from Pellucidar. The others initially dismiss Terk, but believe her after the dinosaur attacks the Professor's camp as well as Tarzan and Jane's treehouse. Tarzan attempts to find out how the velociraptor managed to get out of Pellucidar and how it can be sent back.

Tantor starts believe in an "All-seeing elephant" that protects him after he survives series of dangerous accidents. Tantor decides to journey to Mount Indigo, where the all-seeing elephant supposedly lives, to prove his friends the elephant truly exists. Tarzan, Jane, Terk, and the Professor decide to accompany Tantor to make sure he stays safe.

Tarzan helps the people on an sinking schooner escape. He discovers the passengers are Jane's friends Eleanor, Hazel, and Greenly, as well as Greenly's fiancé Henry. Eleanor and Hazel do not think Henry is "well-rounded" enough, hoping the jungle and Tarzan can toughen him up. Eventually Henry's toughness is put to the test when an earthquake, followed by a tidal wave, hits the jungle.

Count Nikolas Rokoff hears about a treasure in the valley of the leopards and plans to find it. Tarzan doesn't want to help, until Rokoff threatens to hurt Jane if he doesn't.

While the gang is setting up a surprise croquet game for the Professor, Jane encounters an ill-looking fawn. Upon touching the fawn, the soul of Queen La enters her body. Failing to return to Opar by herself, La turns to Tarzan, who senses something wrong right away. Instead, she turns to Dumont for help. Can the aid of Usula, the Waziri elder, bring Jane back before La retrieves her staff and brings Opar to life again?

The arrogant and aggressive heavyweight boxing champion "One Punch" Mulligan, along with his manager and personal journalist, visit the jungle while on safari. When Tarzan accidentally knocks One Punch out cold, the boxer is mortified and demands a "rematch", which Tarzan refuses. However, One Punch is stubborn and looks for a way to provoke Tarzan into a fight.

Philander returns to Africa with two British thugs to capture "Tarzan: The Missing Link" in a last-ditch effort to pay off the thugs. While there, they meet up with the Professor and Philander attempts to convince the thugs that the Professor is Tarzan.

Hugo and Hooft use Tarzan to help them gather special ingredients for their hot sauce. The sauce, with the guys' names on the bottle, becomes popular to the French Foreign Legion, and is brought to the attention of Lt. Col. Staquait. Staquait vows to re-capture Hugo and Hooft for deserting, and succeeds eventually, resulting in the duo being sent to the Cape Doom prison. Upon attempting to free his friends, Tarzan is also captured. Jane attempts to contact the Magistrate to free Hugo and Hooft legally.

Tarzan and Jane attend the wedding of Basuli and Naoh in the Waziri village. As part of the wedding ritual, Basuli must find and return with an eagle's feather. He is allowed a companion and he chooses Tarzan. Their quest is filled with setbacks and Basuli claims that fate is against them. Tarzan, however, suspects sabotage.

Zutho, a shady mandrill from Tarzan's past, resurfaces, demanding a favor he claims is owed for keeping a 20-year-old secret. This results in Tarzan having to do everything Zutho tells him to. What secrets does Zutho know to gain such a hold over the lord of the jungle?

Johannes Niels and Merkus return to the jungle to mine diamonds. Tarzan agrees to this as long as they stay away from the gorillas. Niels and Merkus are threatened by Tublat, who they capture and plan to make money out of him. Tarzan sets out to free Tublat, despite Terk's protests and the past conflict between them.

Clayton's sister kidnaps Jane, Tantor, Terk, and the Professor, placing each in a separate, deadly peril. She then injects Tarzan with a fatal poison via blowdart and informs him that the antidote lies far away on a distant mountain she's dubbed "Clayton's Peak". He, therefore, has a choice—to suffer as she had and lose those he loves, or as Clayton had and lose his own life.

A writer named Ed is in desperate need of some inspiration for his next novel. He finds it while walking down the street in the form of a newspaper article about Tarzan, "The Missing Link". He begins tracking down various leads to Tarzan's whereabouts, including Tarzan's friends and enemies. They all tell Ed of their first encounters with Tarzan, prompting Ed to head out into the jungle to find Tarzan himself.

A violent thunderstorm has Tarzan, Jane and the rest of the gorilla family seeking shelter in nearby caves. Along the way, Tarzan feels unsure that he can protect the family as well as Kerchak did. Upon reaching the cave and thinking they are safe, they realize they are in the same cave where Tublat lives in. Tarzan is no physical match for Tublat and must use his superior cunning and ingenuity to defeat him.