The Bennett family is off to Dr. Fish's new theme park Holiday World. However, their vacation ends when Scarab takes over Holiday World's central computer, sending the park's animatronic Bio-droids on a spree of destruction.

Glove creates a device that can enter the dream world. Once there, he creates a weapons factory to create impossible weapons, which he then brings back to the waking world. Glove's dream merges with Bunji's nightmare.

Professor Sharp's colleague Dr. Bruce "Bad Brains" Huxter creates robotic musicians he calls the Bandroids. The Bionic Six serve as bodyguards to the Bandroids' charity concert. Scarab kidnaps Rock-1 and the Bandroids.

Miners in the Kalahari Desert have been disappearing, so Sharp sends the Bionic Six to investigate. Edward Tulley, mine manager, brings them to the mine. This time, however, the threat is from the new inhabitants of the mine: The Hive.

Dr. Hallowell Patridge, an analytic logic instructor and mentor of both Amadeus Sharp and J.D. has been kidnapped by Dr. Scarab.

After yet another defeat at the hands of the Bionic Six, Dr. Scarab decides to upgrade his Cyphrons. However, the updated Cyphrons now have a mind of their own.

Meg and Bim attend the demonstration of a new invention. When Scarab, Glove, and Madame-O try to steal the device, Bim gets brave and tries to stop them. Scarab captures Bim and Meg, thinking that Bim may be a member of the Bionic Six.

Charlie, a friend of J.D., is awarded student of the year. However, his ceremony is interrupted by a gang called the Nukes. Charlie, who was once a Nuke, rejoins after his award is revoked. It is up to J.D. to stand up for his friend.

Glove, seeking to take over the Scarab Corporation, rigs a stolen Memory-Enhancer to absorb Dr. Scarab's mind. Professor Sharp wants to help his brother start a new, honest life. But Wilbur instead becomes "Scarab to the 10th power".

With his mind wiped and his intelligence boosted, the former Dr. Scarab comes to live in the Bennett household. The Bennett family and Prof. Sharp try to raise him on the side of good but he shows his true colors again.

A recent geologic alert has discovered an abundance of emeralds in nearby Mineral Flats. Sharp sends the Bionic Six to investigate. The heroes encounter "Sparky", a restorer of antique planes.

Prof. Sharp has been tracking a meteor that will impact near the Apennine Mountains on the Moon. Figuring that Scarab will also be interested in it, Sharp enlists the aide of the United Space Center to send the Bionic Six to the Moon.

The Bionic Six are nominated as Crime Solvers of the Year. However, the nomination is objected by Irene Hughes, who challenges the Bionic Six to a competition sponsored by her uncle, a billionaire scientist and fan of Sherlock Holmes.

When Bunji tries a new meditation technique to gain invisibility, the rest of the Bennett kids trick him into thinking it worked. Unfortunately, their trick backfires when a non-invisible Bunji tries to take on Scarab's goons alone.

The team relaxes by visiting a carnival. Once there, Mother-1 visits a fortune teller, who gives her a mysterious prophecy. When the fortune teller's prophecy foretells the truth, and Mother-1's ESP fails, the team is thrown into disarray.

The Bennett family awakens to find a baby on their doorstep, delivered there overnight by two energy beings. The Bennett's new baby is draining light, electrical energy, and bionic energy from all around him.

Meg's effectiveness as a cyborg-superhero is impeded when she's contacted by a microscopic life-form.

The Bennetts' secret identities are threatened when Bunji accidentally videotapes them going into cyborg mode.

The Bionic Six are sent to investigate the emergence of a strange green tar that has erupted from a mining site. Scarab also shows an interest in the tar and the possible Burtonium underneath.

Eric's doubts about a supposedly-reformed criminal-mastermind, with whom the Six have been ordered to work, prove well-founded when he leads them into a deadly set-up.

As King Jonathan ascends to the throne of Fredonia, he is transformed into a giant frog. A second Jonathan arrives, claiming the first to be a demon trying to take the throne. The Bionic Six are sent to investigate.

When Dr. Scarab gets lonely, he decides to create the perfect mate. Scarab realizes that his ideal mate would look like Mother-1. However, his plan to create a mate is sabotaged and he creates a female version of himself.

Scarab and his goons try to steal a Sonic Multiplexer. The Bionic Six arrive on the scene, as does a new "hero" named Captain Confusion.

Dr. Fish returns, this time with a gun capable of rapidly accelerating the growth of fungi. Dr. Fish coincidentally tests his device on the abandoned offshore oil rig directly above Dr. Scarab's hidden lair.

Artificial objects resembling "easter eggs" are hurtling towards Earth from outer space, targeting Undertown, Arizona and Mt. Vesuvius. The Bionic Six must split up to intercept both "eggs".

Prof. Sharp debuts his newest invention, a Time Extraction Device. The device allows Sharp to pull past or future versions of objects into the present. Scarab steals the TED and uses it on himself.

Dr. Scarab and his team set up his Modifier. Though the Bionic Six arrive on the scene, they are too late to prevent Scarab's Modifier from activating, covering the entire Earth in an energy wave. Now the world is under Scarab's rule.

In two days time, the effect of scarab's Modifier will become permanent, and everybody in the world will worship him. Prof. Sharp sends his new Bionic Six after the original Bionic Six, whom Scarab has imprisoned around he world.

Sharp introduces the Bionic Six to his old friend, Nicholas Nicholby, the world's foremost illusionist. Scarab, thinking that Nicholby's abilities are the result of real magic, kidnaps Nicholby.

Prof. Sharp creates a Parallel Dimensional Viewer, with which he can view parallel dimensions. J.D. offers to help fix a glitch in the system, and when he does so, he accidentally allows a creature from a parallel world to cross over.

He Bionic Six are taking an underwater tour of the Marianas Trench, scouting a test location for Prof. Sharp's new invention the Gravitron. Scarab makes an attempt to steal the Gravitron.

Scarab sends his goons below ground in Arizona to mine for Burtonium. Glove convinces the rest of the goons to head above ground to rob some of the locals. They are thwarted by a new super hero with the ability to manipulate the elements.

An experimental radar-defeating automated stealth plane prototype named Viper has crashed landed on a remote island in the south Pacific. Viper's AI programming is severely damaged, making it attack the Bionic Six.

A crooked boxer named Joe Kapula tries to get a cut of money from the dive he just took. Offering him a position on his team, Scarab offers Joe a job and transforms him into the Shadow Boxer.

The Bennett family throw a surprise party to Bunji. One of his presents is delivered by a hologram of his father which tells him that he is ready for the next step in his path to enlightenment: He must travel alone to the Himalayas.

Prof. Sharp has transformed his Parallel Dimensional Viewer (PDV) into a Parallel Dimensional Portal (PDP). The Bionic Six must deliver the PDP microchip to Dr. Mabusa at the Science Research Council but Glove steals the PDP chip.

An unknown spacecraft from outside the Solar System is heading towards Earth. The spacecraft lands in front of the U.N. building, revealing its inhabitant: a sentient, English-speaking monkey who came with an important mission.

The Six must prove their worth to a government higher-up whose proposed budget cuts would put them out of action as international troubleshooters.

Famed underwater archaeologist Jonathan Dryden discovers the lost city of Melodius off the coast of Greece. Madame-O uses an ancient harp from the treasures on Scarab, which causes him to fall in love with her.

Dr. Scarab steals the Omega Amplifier, a hand-held machine capable of controlling electricity. However, Scarab's latest plan is delayed when a stray dog taken in by Mechanic runs away with the Omega Amplifier.

When Mechanic drops off a load of toxic waste in a junkyard, he accidentally creates a sentient junk heap creature. This creature, called "Junk Heap", can absorb other forms of matter and energy into itself.

Scarab has developed a way to move his team's brains into new, indestructible bodies. Scarab's goons head to Polymorph Plastics to get the last component he needs to complete the new bodies.

J.D. and Bunji attend the retirement party for the greatest cartoonist in the world, Flub Fleming. Fleming announces that he is not retiring, but rather was forced out. He then steps through a wormhole into a world of cartoons.