Explorer Brent Holworth returns from the Valley of Shadows, a hidden jungle valley where it is rumored its inhabitants never age. Holworth notifies Professor Sharp, but immediately afterward is captured by Scarab. The Bionic Six and Scarab's team both race to find the Valley of Shadows first.

Scarab's goons gather information about Dragon's Rock, a remote island in the East China Sea. Each year, the greatest martial artists gather on Dragon's Rock to compete in the Grand Master's Tournament. Prof. Sharp sends Karate-1 undercover to discover Scarab's plans. Karate-1 also hopes to use the opportunity to find his missing father, who he thinks may be on Dragon's Rock.

Prof. Sharp informs the Bionic Six that a meteor is on a collision course with earth in New York City. I.Q. estimates the impact will explode with the force of a 10 megaton bomb. Meanwhile, Dr. Scarab has discovered that the meteor contains a large amount of Bertonium, an element that can help him achieve immortality. He sends Chopper, Glove, and Mechanic to retrieve the meteor.

While on an underwater excursion, Mother-1 discovers a fissure to a hidden world, where all the aquatic creatures share a mental link. Mother-1's telepathy allows her to communicate with an octopus-like creature, convincing her to come with Mother-1 to our world. When Scarab sends Madame-O and Klunk to investigate this new fissure, Klunk falls in love with the mysterious octopus-creature.

Dr. Scarab creates a radio station: Radio Scarab. Using the station as a cover, Scarab transmits a frequency that jams bionics. During family training, Scarab's signals interfere with Karate-1's bionics, causing him to accidentally injure a non-bionicized Meg Bennett.

When Prof. Sharp learns of the death of his aunt Hilda Millicent Howell, he is invited via teleconference to listen to a video of her last will. Dr. Scarab is also invited to watch, and both Sharp and Scarab are asked by the now-deceased Aunt Hilda to become friends. Little does Sharp realize that Hilda's death is a trick by Scarab.

The Bionic Six plan a surprise party for Prof. Sharp's birthday. Dr. Scarab has the same idea, and he and his goons break into Prof. Sharp's museum. Karate-1 decides to surprise Sharp by disguising himself as Dr. Scarab. Scarab discovers Karate-1's plan, and swaps himself with the disguised Karate-1.

Dr. Hugo Fish creates a food capable of increasing a creature's intelligence by tenfold. Dr. Fish decides to debut his creation at the Paris Food Conference. Unknown to Fish, Madame-O steals a sample of his Brain Food and gives it to Scarab. Scarab sends Glove and Madame-O to steal more, where they are intercepted by the Bionic Six.

Prof. Sharp and the Bionic Six appear at the Sheldrake Academy, where Sharp debuts his Anti-Gravity Glide Path Controller. In addition, Sharp designs various pieces of equipment for disabled children. One student, Ronnie Gordon, shows his bitterness to the team, and Scarab's group convinces him to turn on the Bionic Six. Ronnie lures I.Q. into a trap, and he is captured by Glove and Madame-O, who hold him hostage in exchange for the controller.

Jack Bennett had taken his family on a skiing trip to the Himalayas. During this trip, Jack is called to duty to investigate unusual magnetic readings. He encounters aliens who are trying to obtain Burtonium, a mineral that can increase bionic abilities and give eternal life to its possessor. In a battle, Jack's family becomes trapped under radioactive snow and they slip into a coma. Not seeing another way to save their lives, Jack permits Professor Sharp to operate on his family. Professor Sharp implants bionics in human beings, and the Bionic Six are born. Doctor Scarab creates his own bionic group from "worthless examples of humanity."

Prof. Sharp builds a Perpetual Chronographic Generator, a machine that will allow time travel. As Sharp prepares to send the Bennett family and Drs. Lund, Swift, and Johnson back in time to the Mesozoic Era, the group is attacked by Scarab's goons. Glove, Mechanic, and Madame-O trade places with the doctors, and sneak into the past with Mother-1, Sport-1, and I.Q.

Due to Glove's interference, dinosaurs from the Mesozoic Era pour through Prof. Sharp's Perpetual Chronographic Generator in the Mojave Desert. While Bionic-1, Karate-1, and Rock-1 deal with the dinosaurs in the present, Mother-1, Sport-1, and I.Q. must deal with Scarab's goons in the past. With fights in two different time periods, Prof. Sharp must repair the time generator before it creates a permanent rift in the "time-flow continuum".

Cycron the Great, a Voltron-like television show, is a favorite of both F.L.U.F.F.I. and the Mechanic. When the Mechanic realizes that Cycron is really an actor, Mechanic traps the actor and replaces him. Mechanic-Cycron tricks F.L.U.F.F.I. into doing his bidding, which includes stealing cute puppies and robbing banks.

When Scarab attacks a microwave receiving station, the Bionic Six arrive to stop him. However, Scarab's attack was just a ploy in order to capture Sport-1. Once captured, Scarab tricks Sport-1 into thinking he is 30 years in the future after suspended animation, and that Scarab is good while the Bionic Six are evil.

After Rock-1, Sport-1, and I.Q. intercept Klunk in a Punjabi bazaar, Rock-1, as Meg Bennett, returns to attend the Socrates Hop at Albert Einstein High School. However, Meg's desire to go with Bim is thwarted when Bim asks Janet Sutton out first. Meg gets frustrated after being asked out by Furty Fosberry (a geeky freshman) and Dr. Oscar DeLeon (a fourteen-year-old scientist). However, Dr. DeLeon holds a secret ... one that Scarab desires.

The Bennett family get tickets to the Old Timers' Game at Yankee Stadium. Retired baseball player Homer Hernandez returns for the game after a disappearance of 30 years. However, it appears that Hernandez has not aged a day. This "eternally young" baseball player draws the attention of Dr. Scarab.

Prof. Sharp receives a message from Momo Yashima, an ally of Karate-1's from Dragon's Rock. The Bionic Six travel to Momo's village in Japan, where they must protect the village from the threat of the Ancients, ghosts from the past. The Ancients are angered because someone unworthy has desecrated the Armor of Light in the Temple of the Lost Samurai.

Professor Sharp and a team of archaeologists discover the ancient Scarab Scroll: a map to an ancient treasure. Bionic One turns over command of the team to the kids for 24 hours, and the kids must learn how to work together before Dr. Scarab gains control the Crown of the Scarab King.

When all technology in the Middle Eastern nation Shariar dies, Professor Sharp sends the team to investigate. Once there, Mother-1 is kidnapped by A.L.A.D.D.I.N. (A Logistical Analytical Dream Drive with Improbability Neurons), a sentient reality-altering computer that requires the feeding of "more data".

A strange man calling himself the "Perceptor" declares a one-man war on technology. His sabotage of Professor Sharp's newest aircraft brings him to the attention of Bionic-1. However, when the team discovers that the professor is covering for the vigilante, they realize there is more than meets the eye about the Perceptor.

Dr. Fish unveils his latest invention: the Fish Art Demolecularizer (or FAD). His device is able to absorb a masterpiece of art, then via a headset, instruct a person to recreate it. Chopper and Mechanic try to kidnap Dr. Fish, but are stopped by the Bionic Six. However, unknown to the Bionic Six, Dr. Fish was actually replaced by Glove during the hijack attempt.

When Bionic-1 and Mother-1 leave for a vacation in Honolulu, the kids have the house to themselves. The kids try to keep their identities secret while throwing a house party, but that becomes much harder when Scarab and his goons crash the party.