Sebastian has secretly formed an evil rebellion to get revenge on the Lab Rats for destroying his father. Meanwhile, Leo is trapped with the other bionic people who also want revenge, but Leo manages to convince Spin and Bob to help him, and, in the end, Sebastian is defeated, his rebellion is brought down, and he and his comrades are taken to a facility. Meanwhile, Donald successfully convinces the others that he has the best interest for them at heart while Adam still blames Chase for everything that happened after the rebellion is over.

Sebastian has secretly formed an evil rebellion to get revenge on the Lab Rats for destroying his father. Meanwhile, Leo is trapped with the other bionic people who also want revenge, but Leo manages to convince Spin and Bob to help him, and, in the end, Sebastian is defeated, his rebellion is brought down, and he and his comrades are taken to a facility. Meanwhile, Donald successfully convinces the others that he has the best interest for them at heart while Adam still blames Chase for everything that happened after the rebellion is over.

After sneaking some students off the island and to the mainland, the Lab Rats accidentally leave Spin and Bob behind and must retrieve them before Donald finds out. Meanwhile, Donald tries on Chase's mission suit and he and Leo scramble to get it off before Chase gets home.

When suspicious events happen overnight on the bionic island, everyone is convinced a new threat has emerged. However, this threat is revealed to be Leo, when his bionics glitch because Douglas never gave Leo a capsule.

Adam brings a dog back to the island and Douglas reveals that it's his old dog, Otis, who Douglas made bionic in order to save his life when Otis was injured. Chase turns out to be allergic to dogs as he starts sneezing, so Douglas says that Otis has to leave, but he and Adam actually hide the dog. Meanwhile, Leo gets a new smartphone application assistant named Shelly, with whom he has fallen in love.

The Lab Rats are on a mission to save people from a wildfire; when the people start to chant Adam, Bree, and Chase's names, Leo gets jealous and wants to become known. Douglas gets put in charge to develop a new technology for the academy, but can only come up with things that can hurt the students.

Adam and Chase each lead their own student groups against each other in a series of simulated exercises that will evaluate both student and mentor performance. However, after Chase's group fails at defeating the exoskeleton and defusing a virtual bomb, Chase decides to find a way to cheat and win.

When Leo is injured during a mission, Tasha rushes to the academy to take care of him. After finding out what happens on missions, she bans Leo from joining any more missions, but he disobeys her and goes on a mission with the rest of the team. When Tasha finds out, she kicks Leo off the team and tells him that he is moving back to Mission Creek.

Chase and Douglas reanimate a prehistoric sea spider. It escapes and bites Adam, which poisons him. It then grows and becomes 50 feet long due to growth hormones that had been given to it by Douglas. Everyone tries to stop the spider so they can create a cure for Adam.

Douglas finds out that there is a student named Kate with the Commando App. Chase tries to activate her Commando App, named Spikette by Douglas, so he can research her. When he starts fighting with Adam, she activates her Commando App and thinks Chase is her baby. While she destroys the bionic academy, Bree forces Chase to activate his Commando App by embarrassing him so he and Kate can battle. Unfortunately, he teams up with her. Douglas gives Bree a Commando App and she and Kate begin battling each other. Bree wins and Douglas extracts Kate's chip. Chase apologizes to Kate and finds out that Douglas replaced her Commando App with sonic screaming.

Donald's top scientist, Dr. Ryan, arrives to test Chase's invention. The two of them dislike each other and don't get along. When Donald puts Dr. Ryan in charge of the space elevator, Chase immediately gets jealous. Donald then makes Chase Dr. Ryan's assistant. Dr. Ryan puts Chase in charge of screwing in the lug nuts, but Chase refuses, and Dr. Ryan builds the space elevator without Chase. The day of the launch, Chase performs a bionic scan of the elevator and finds a major braking flaw on the elevator.

Douglas tells the group that his old college ex-girlfriend, a film director named Giselle, will be making a film titled Bionic Action Hero based on all of them and starring an up-and-coming actor named Troy West. Giselle and Troy visit the island to learn about the bionic team.

Douglas tells the group that his old college ex-girlfriend, a film director named Giselle, will be making a film titled Bionic Action Hero based on all of them and starring an up-and-coming actor named Troy West. Giselle and Troy visit the island to learn about the bionic team.

Adam, Bree, and Chase are looking for Leo because he is late for training and find out he is in Mission Creek because Janelle threatened to break up with him. S-1 shows up unexpectedly and shocks everyone. She came to the island because, like everyone else, her memory is blank, but has continuing flashbacks of Krane.

Douglas creates a device that makes any bionic human as smart as Chase. After Douglas tests it on Bob, Bob starts spending time with Chase. This leaves Adam in envy. Meanwhile, Perry made the island officially her own, which makes Bree and Leo angry at her.

Donald gives Eddy a human body and replaces his disrespectful personality to make him nicer. Perry restores his old personality, and he attempts to harm the students.

Leo just finishes his movie marathon while everyone else is frustrated because they have nothing to do on Halloween. Bob intentionally stays behind while the other students are away with Davenport to a museum. Perry says she's going to another island across from theirs, but Douglas says no because it's deserted and has been uninhabited for years. When Douglas leaves, the group decides to go anyway.

Donald tells the group that the president has decided to host an award ceremony because they have completed their one-thousandth mission and Leo wants his recognition, but it's only for the original members. Disappointed, Leo forms his own team with S-1, who calls herself Taylor now, and Logan.

Tasha arrives on the Bionic Island informing everyone that she has tickets to a big football game of the Pioneers (mascot of a college that she went to) vs Vikings (mascot of a college that Perry went to) and Perry arrives stating that she has been trying to score tickets for weeks but it was sold out. When she asks Tasha if she has any tickets, Tasha lies saying that she hasn't. When they are about to enter the game, Perry eventually finds out the truth, she becomes furious and destroys the tickets which causes Leo, Donald, and Tasha to try to get new tickets competing against her in The Ultimate Tailgate Challenge, hosted by NFL former linebacker Willie McGinest. Meanwhile, Bree attempts to achieve her college experience by fitting in with a couple of college students (who are football fans) and attempting to use her bionics to impress them.

Everyone is shocked when Douglas introduces a fourth bionic sibling named Daniel who’s been living a normal life with an adopted family. Daniel later comes to the academy to meet his father, uncle, and cousins. After Daniel's bionics are accidentally activated by the Lab Rats, Donald and Douglas find out what happened they have to come clean to Daniel about his power-replicating abilities. Daniel also finds out that his cousins are actually his biologic siblings. Filled with anger, Daniel goes out for air on the beach, where Leo and him have a conversation about Douglas. Not too long after, Daniel, using Leo's abilities, accidentally causes a leak in the hydro-loop's fuel tank. After Adam and Daniel combined their powers to stop it, Douglas apologizes to Daniel for lying and Daniel decides to give Douglas a second chance.

In the middle of a massive heat wave, the whole family is going to space to see Donald's space colony, called "Davenportia". Adam annoys Chase while Chase tries to give his safety instructions and accidentally blasts them into space. After leaving the solar system, they initiate hyper-speed and land on the planet Lithios. In the dome, it's discovered that Perry sneaked her way in with the rest of the colonists.

Donald and Douglas reveal that they have built an upgrade for all the students bionics, except for Leo's. But the upgrade doesn't work on Adam, Bree, and Chase because their systems are older. Adam, Bree, and Chase are therefore left at their level, while all the students are much more powerful. Meanwhile, Daniel is brought to the Academy because he had been using his bionics in the outside world. Douglas decides to enroll Daniel at the Academy, and he makes Leo his mentor. Leo steadily tries to teach Daniel, but Daniel proves to be unteachable, so Leo gives him the upgrade as well. The students steadily start to vanish, including Daniel. Giselle Vickers, Douglas' old girlfriend, is revealed to have captured them. Daniel sends a video message to the Island, requesting help.

Giselle reveals she dug up Marcus from Douglas' old lair and rebuilt him, piece-by-piece. Marcus wants revenge on Douglas for leaving him to die. Everyone rushes Giselle and Marcus, but Marcus knocks everyone unconscious. Donald and Douglas are tied together in chairs, while Adam, Bree, Chase, and Leo are put in the chamber with the students, while Daniel is pulled out.