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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, and with the help of the ghost of Bunji's father, Bunji guides the team to stop Glove.

Professor Sharp's colleague Dr. Bruce "Bad Brains" Huxter creates robotic musicians he calls the Bandroids: guitarist Rivet Rick, keyboardist Techno Tex, bassist Metalhand, and drummer Bob. The Bionic Six serve as bodyguards to the Bandroids' charity concert. Scarab kidnaps Rock-1 and the Bandroids, intending to reprogram the band into his unwitting accomplices in his goal for eternal youth.

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. The Bionic Six do not realize that Tulley is actually on Scarab's payroll. This time, however, the threat isn't from Scarab; it is from the new inhabitants of the mine: the Hive.

Prof. Sharp's colleague Dr. Halliwell Partridge is kidnapped by Chopper. Scarab has a new plan: kidnap four of the greatest analytical thinkers and connect them to Scarab's supercomputer. With three scientists in place, Scarab targets his fourth: Bionic Six member I.Q.

After yet another defeat at the hands of the Bionic Six, Dr. Scarab decides to upgrade his Cyphrons. The new Beta Cyphrons are programmed to think for themselves, and are programmed with the tactics of the greatest military minds of history. Scarab sends the new Beta Cyphrons after the Bionic Six while he steals Sharp's new Ultra-Beam Laser. However, the Beta Cyphrons now have a mind of their own.

After Prof. Sharp creates a Bio-Energy Replicator, he debuts this new invention. Meg Bennett and Bim attend the demonstration to interview Prof. Sharp for their science project. When Scarab, Glove, and Madame-O try to steal Prof. Sharp's 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.

At Albert Einstein High School, Charlie Wilder, a friend of J.D. Bennett, 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. When J.D. investigates, he finds out that Scarab is instigating a gang war between the Nukes and a rival gang, the Lasers.

Prof. Sharp creates a Memory Enhancer, a device that can increase a person's memory by 75%, and demonstrates it for the government. However, Scarab creates a "Memory Enhancer Enhancer", which will increase the capabilities of Sharp's machine even further. The Bionic Six and Scarab clash over the Memory Enhancer, and Scarab uses it on himself, not knowing that Glove sabotaged it. Scarab's mind is wiped, and Sharp takes the opportunity to re-teach Scarab everything, hoping Scarab will end up on the side of good.

With his mind wiped and his intelligence boosted, Wilmer Sharp (the former Dr. Scarab) comes to live in the Bennett household. The Bennett family and Prof. Sharp try to raise Wilmer on the side of good. Wilmer shows his true colors again, but becomes even more threatening when he discovers the secret identities of the Bionic Six. He then "takes over" his former gang and sets his sights on the Bionic Six.

A recent geologic alert has discovered an abundance of emeralds in nearby Mineral Flats. Professor Sharp sends the Bionic Six to investigate. The heroes encounter "Sparky", a restorer of antique planes. They agree to help Sparky raise money by putting on an antique air show. Scarab realizes that the antique aircraft Lulubelle, a B-25 bomber, was lost with a load of emeralds. Scarab's team sets out to steal the aircraft.

The Bionic Six are nominated as Crime Solvers of the Year by the Crime Solvers Society. However, the nomination is objected by Irene Hughes, citing that the Bionic Six solve crimes with brawn rather than brains. She challenges the Bionic Six to a competition sponsored by her uncle Mycroft Hughes (a billionaire scientist and fan of Sherlock Holmes). Karate-1 and I.Q. accept, but Scarab and Madame-O crash the party.

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 single-handedly. When Karate-1 gets captured, the Bionic Six and the ghost of Bunji's father come to his aid.

After the Bionic Six responds to an avalanche at the High Mountain Ski Resort in Colorado, 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. Unbeknownst to the team, Scarab and Madame-O are behind Mother-1's ESP failure.

The Bennett family awakens to find a baby on their doorstep, delivered there overnight by two energy beings. Scarab, discovering the night before an interdimensional doorway opened, travels to Cypress Cove to investigate. Meanwhile, the Bennett's new baby is draining light, electrical energy, and bionic energy from all around him.

During a battle against Madame-O and Klunk, Rock-1 becomes distracted by a voice in her head calling for help from the Bionic Six. Prof. Sharp discovers the source of the sound: a distress call from a sub-atomic anti-matter world. Rock-1, Sport-1, and I.Q. are transported to a sub-atomic ship by Captain Stereopolis. The captain's world is being destroyed by Scarab's current experiment. The Bionic Six must stop Scarab's anti-matter experiment.

Bunji has taken up a new hobby: 3D Laser Holo-Filmmaking. One of his first projects becomes a film documenting the life of the Bennett family. Unfortunately, Bunji's camera accidentally captures the Bennett family transforming into the Bionic Six. A mix-up has Mechanic getting a hold of the disc with the Bennett family's secret identities. Karate-1 and the rest of the Bionic Six must now track down Mechanic and the missing disc.

The Bennett kids and Prof. Sharp meet up with Hokey McCoy, an old time con artist and friend of Prof. Sharp. Afterwards, 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), and assaults the mining site. Scarab captures the tar pit, and sets up an anti-bionic field. Sharp calls upon Hokey's skills to con Scarab into giving up the site.

Prof. Sharp's computer intercepts a signal from Scarab's computer with the mysterious message "Reactivate Project Mars". 20 years ago, when Dr. Scarab first embarked on a life of crime, he partnered with a master of disguise named Kaleidoscope. Their last caper, Project Mars, was left unfinished. Now, the Bionic Six must contact Kaleidoscope in jail to discover the truth about Project Mars.

As King Jonathan ascends to the throne of the fictional nation 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 whole scheme was orchestrated by Scarab in order to close Fredonia's border and use Fredonia's export of unique microcircuits. The Bionic Six are sent to investigate.

When Dr. Scarab gets lonely, he decides to create the perfect mate. Using his computer, Scarab realizes that his ideal mate would look like Mother-1. Scarab plans an ambush, and kidnaps Mother-1. However, his plan to create a mate is sabotaged by Madame-O, and the result is an identical female version of Scarab.