Leo and Donald escape the elevator. Principal Perry lets them stay at the school temporarily in order to get her money from Donald quicker. The Lab Rats stow away on a cargo ship to hide from the FBI and must choose to either keep quiet or help stop a submarine that will crash into the ship and risk being caught. The Lab Rats decide to stop the submarine, with Chase activating his GPS, revealing the Lab Rats' location. Douglas ends up capturing them, disguised as Donald. Douglas reveals that his new bionic partner is a billionaire named Victor Krane, who wants to destroy the Lab Rats permanently. When Donald calls the Lab Rats and tells them that Principal Perry kept their secret, they return home, only for them to get crazy as a result of the Triton App and attack the family, Leo manages to disable Chase's Triton App when he talks to him and Chase manages to disable Adam and Bree's apps. The Lab Rats and the family later see the demolition that happened to the lab and are upset.

Leo and Donald escape the elevator. Principal Perry lets them stay at the school temporarily in order to get her money from Donald quicker. The Lab Rats stow away on a cargo ship to hide from the FBI and must choose to either keep quiet or help stop a submarine that will crash into the ship and risk being caught. The Lab Rats decide to stop the submarine, with Chase activating his GPS, revealing the Lab Rats' location. Douglas ends up capturing them, disguised as Donald. Douglas reveals that his new bionic partner is a billionaire named Victor Krane, who wants to destroy the Lab Rats permanently. When Donald calls the Lab Rats and tells them that Principal Perry kept their secret, they return home, only for them to get crazy as a result of the Triton App and attack the family, Leo manages to disable Chase's Triton App when he talks to him and Chase manages to disable Adam and Bree's apps. The Lab Rats and the family later see the demolition that happened to the lab and are upset.

Since the lab is destroyed, the Lab Rats go without their capsules. This causes glitches in their bionics. In order to prevent this, Donald pulls off a huge stunt in a fiberglass jet wing he invented. Things go wrong when the jet wing runs out of fuel. Meanwhile, knowing the Lab Rats' bionic secret, Principal Perry uses Adam and Bree as her bionic servants for the day.

Since Principal Perry knows that the Lab Rats are bionic, she wants to get in the action and go on a mission with them. When they stage a fake mission and take her down to the newly built lab, things don't go as planned, and they have to save Mission Creek High from a speeding rocket. Meanwhile, Janelle goes on a date with Leo, but is beginning to see him as a jinx because she always gets hurt when he is around.

Bree gets a part-time job at a tech-support store with Caitlin, but gets out-shined by Chase while he is talking to the manager of Tech Town, Scott. Chase sees how she feels later and they agree to treat each other with respect. Meanwhile, while Tasha is away visiting Grandma Rose, Leo and Adam make a turbo zip-line instead of doing the chores that Tasha gave them, with Donald joining them later. When Tasha finds out about the zip-line, she makes the boys do the chores and she hangs out on the turbo zip-line instead, much to the dismay of Adam, Leo, and Donald.

Chase loses the phone with a bowling video of him and Adam doing bionic bowling stunts at Tech Town while working. Leo and Bree try to get Principal Perry to spend her money when she retires after Donald gives her money and Trent becomes the principal and makes Leo's life miserable. It works in the end, but Principal Perry is broke and Scott fires Caitlin after she destroys an ePhone 7, the one that had Adam and Chase's bowling stunts on it, while giving them to the customers as revenge. Leo makes Trent wear a different uniform, but to Bree and Leo's shock, he loves it, much to their dismay.

Leo invents his first high-end technological creation, a pair of attack orbs meant to protect the family, but when they can't differentiate between friend and enemy, they create more bad than good. Meanwhile, Chase steals Donald’s Eddy technology to make a Cheddy application to win a Tech Town employee contest and beat Scott, but things go wrong when the technology doesn't work as expected. Leo and Tasha go to see Janelle's play which Adam is starring in, but when Trent steals Leo's ticket, Leo and Trent ruin her play, much to Adam and Janelle's dismay.

During a lunar eclipse, Principal Perry arrives at the house to inform everyone that aliens are on the planet, much to the cha Bree, Chase, and Donald's chagrin, but Adam and Leo's shock. She insists that Chase's upset stomach is due to an alien growing inside him and chases him. However, they notice green goop leaking out of Principal Perry's ears and mouth. Donald then admits that she's an alien. Principal Perry chases everyone, while Leo records the whole thing, and eventually tires herself out. Leo accidentally wakes her and she runs off with him to the school. Adam's heat vision destroys the alien pods Principal Perry laid and Leo is freed. The mother ship beams Principal Perry away just as Donald arrives. Thinking that they will miss Principal Perry, they are sadly mistaken when the mother ship beams alien-less Principal Perry back down. It is then revealed the whole thing was Leo's entrant in a contest.

Donald shows a new motorcycle to the Lab Rats when they get a video message from Douglas that Krane has lost it and implanted himself with more bionic abilities, abilities even he doesn't know about. The Lab Rats instead believe this to be a trap, leading Donald to activate a new security system that only he can bypass. While Leo is at Mission Creek High School, Douglas arrives and tries to appeal to Leo by reminding him that he knew about Douglas and Marcus before the rest of them. Douglas then shows Leo video footage of Krane implanting himself with bionics and asks him to call his brother to prove his honesty. Back at the lab, a transmission comes in and shows Leo and Tasha captured. While Donald thinks it's Douglas, Krane reveals himself on-screen as the captor and demands that the Lab Rats arrive in 10 minutes. While the Lab Rats want to rescue them, Donald heads out alone with an extremely powerful thermal blaster. Donald arrives at Krane's lair, only for Krane to siphon the power from the blaster, rendering it useless and quickly beating Donald with super strength and molecularkinesis. During the battle, Leo and Tasha are trapped in an exothermic energy field to fry them. Afterward, Krane geo-leaps to the lab, allowing Donald to use the thermal blaster to suck in the heat to set Leo and Tasha free. As Chase works to deactivate the security system, Krane arrives and easily beats the Lab Rats with his more advanced bionics. Before Krane can finish them off, Douglas arrives and blasts Krane with a laser blaster. Although he saves the Lab Rats, Krane quickly recovers and knocks him down with another force wave. As he once again prepares to attack, Chase repels his blast back at him with a force-field, defeating him for good. Douglas plans to capture the unconscious Krane, but Donald arrives and blames the entire mess on him. Unfortunately, Krane geo-leaps out of the house and Donald demands that Douglas leaves.

Bree is accepted for a semester abroad program in Australia, but when Donald learns about it, he refuses to let her go. When Donald again refuses to let her go to a concert with her friends in favor of bionic chip maintenance, she decides she's had enough and smashes her bionic chip, much to Adam, Chase, and Donald's horror. At first, Bree relishes her new freedom and even begins bragging to a disgruntled Leo. During a mission, Bree feels helpless as Adam and Chase are gone for hours. Chase reveals that they barely made it out alive and because Bree is no longer bionic, the mission took twice as long. Bree realizes she was selfish and apologizes to Adam and Chase. She's ready to become bionic again, but Donald sadly tells her that since Douglas built the chips, he isn't sure if Bree will ever be bionic again. Meanwhile, Tasha is sick, so Leo decides to use his new pill invention on her to see if her diagnosis will reveal the problem, but when he takes some of the software from Eddy, Eddy is stuck in Tasha's body. Eddy spends the day dressing her horribly and getting her kicked out of every spot in town. Donald finally uses his nasal vacuum on Eddy and the pill is extracted. However, Eddy reveals he did a news report as Tasha, and much to her shock, he made her look like a complete buffoon.

As Donald attempts to repair Bree's damaged chip, the replacement chip keeps malfunctioning, much to Donald's frustration. Although Leo believes Douglas can help since he was the original creator, Donald refuses to even see his brother again. Realizing Donald won't change his mind, Leo finds Douglas, anyway, who reluctantly agrees to help. While Donald is away, Douglas creates a new chip as close to the original as possible, and though it seems to work, it also malfunctions by causing Bree to run uncontrollably. Donald finds Leo with Douglas at the lab, but helps out and all three manage to keep Bree still; however, they still can't find a solution. After several minutes, they finally find the error and collaborate for the first time in years, fixing Bree's chip and saving her life. Meanwhile, Adam and Chase try to find a way to replace Bree's speed. While Chase manages to power up Donald's motorcycle to go 350-400 MPH, it runs out of gas almost instantly. After Bree's chip is fixed, Donald still kicks out his brother. While watching Bree apologize for her mistake, Donald realizes everyone deserves a second chance. The next morning, Donald offers his brother a chance to move in with them temporarily, and he accepts.

Leo's scared by a shark movie, so Adam and Chase use one of Donald's sharks to scare him, but it goes haywire and Adam, Chase, Leo, and Janelle end up stuck in the house. In the end, Leo turns the sharks off. Meanwhile, Principal Perry enlists Bree and Donald's help to get into a country club, but when she lies that Donald is her husband and Bree is her daughter and they have pottery around the world, Bree must use super speed to go places without the country club owner knowing about her bionics. Eventually, Principal Perry doesn't get in after the manager figures out the lies, but she decides to spend the summer with the Davenports.

When the Lab Rats are on a mission, it is revealed that a girl was secretly recording them behind a bush. The next day, the Lab Rats go to school and everyone is looking at a viral video called The World's First Bionic Humans. They go back home to tell Donald, but he says he already knows. Meanwhile, Chase is confused that he didn't notice the girl who filmed them behind the bush, even though he thermal scanned the whole place. He then looks at a chip log and finds out that the girl was in the exact spot he scanned. Chase then goes to tell Donald, but a swarm of government agents surrounds them. Leo and Douglas are still in the lab, but they use a trap door to escape and go to school to stay safe. It is then revealed that the mission the Lab Rats were on was a setup. Krane then shows up with the girl who filmed the Lab Rats, whose name is revealed to be S-1. It is also revealed that she is bionic. Krane electrocutes Principal Perry and Douglas while S-1 crushes Leo's arm. Later, Douglas and Principal Perry help Leo to get his arm fixed and take him to the hospital. Tasha later shows up, only to realize that Leo is gone. While the Lab Rats are saying their goodbyes, Special Agent Graham tells them it's time to leave, but Adam refuses. Agent Graham orders his agents to take them down, but Adam uses his wave blast ability to knock them down. When they run to the hospital, Principal Perry tells them Krane is responsible for exposing their bionics. Meanwhile, Leo is in Douglas and Krane's old warehouse and Douglas tells him to take his bandage off and pretend to throw a ball. He then realizes that Douglas upgraded his right arm with bionics. Krane then shows up and knocks down Leo and Douglas. The Lab Rats then show up with Donald, as Krane uses a powerful bionic ability that knocks out Leo, Donald, and the Lab Rats. Krane then paralyzes Donald with his choking ability. Bree battles S-1 while Adam and Chase battle Krane, but he easily takes them down with his newly upgraded Triton App that he uses on S-1. Leo then uses his bionic arm to take down Krane. As Agent Graham arrives, Douglas reveals that Krane and S-1 are the bionic villains. Agent Graham is then saved by Bree as Krane tries to attack him and he takes Krane and S-1 into custody and locks them in a prison with a bionic signal interrupter, preventing them from using their bionics to get out. Later, the Lab Rats are at a press conference and reveal that they are bionic superhumans. While watching it, Principal Perry makes new friends with the Lab Rats. In the end, Agent Graham tells Donald he's now in charge of the Lab Rats. It is also revealed that Krane has an army of bionic soldiers, which he will use to destroy the Lab Rats.

When the Lab Rats are on a mission, it is revealed that a girl was secretly recording them behind a bush. The next day, the Lab Rats go to school and everyone is looking at a viral video called The World's First Bionic Humans. They go back home to tell Donald, but he says he already knows. Meanwhile, Chase is confused that he didn't notice the girl who filmed them behind the bush, even though he thermal scanned the whole place. He then looks at a chip log and finds out that the girl was in the exact spot he scanned. Chase then goes to tell Donald, but a swarm of government agents surrounds them. Leo and Douglas are still in the lab, but they use a trap door to escape and go to school to stay safe. It is then revealed that the mission the Lab Rats were on was a setup. Krane then shows up with the girl who filmed the Lab Rats, whose name is revealed to be S-1. It is also revealed that she is bionic. Krane electrocutes Principal Perry and Douglas while S-1 crushes Leo's arm. Later, Douglas and Principal Perry help Leo to get his arm fixed and take him to the hospital. Tasha later shows up, only to realize that Leo is gone. While the Lab Rats are saying their goodbyes, Special Agent Graham tells them it's time to leave, but Adam refuses. Agent Graham orders his agents to take them down, but Adam uses his wave blast ability to knock them down. When they run to the hospital, Principal Perry tells them Krane is responsible for exposing their bionics. Meanwhile, Leo is in Douglas and Krane's old warehouse and Douglas tells him to take his bandage off and pretend to throw a ball. He then realizes that Douglas upgraded his right arm with bionics. Krane then shows up and knocks down Leo and Douglas. The Lab Rats then show up with Donald, as Krane uses a powerful bionic ability that knocks out Leo, Donald, and the Lab Rats. Krane then paralyzes Donald with his choking ability. Bree battles S-1 while Adam and Chase battle Krane, but he easily takes them down with his newly upgraded Triton App that he uses on S-1. Leo then uses his bionic arm to take down Krane. As Agent Graham arrives, Douglas reveals that Krane and S-1 are the bionic villains. Agent Graham is then saved by Bree as Krane tries to attack him and he takes Krane and S-1 into custody and locks them in a prison with a bionic signal interrupter, preventing them from using their bionics to get out. Later, the Lab Rats are at a press conference and reveal that they are bionic superhumans. While watching it, Principal Perry makes new friends with the Lab Rats. In the end, Agent Graham tells Donald he's now in charge of the Lab Rats. It is also revealed that Krane has an army of bionic soldiers, which he will use to destroy the Lab Rats.

Leo tries to show off his bionic arm to Janelle. Meanwhile, Agent Graham promotes the Lab Rats as bionic celebrities, but when they realize they missed a mission because of him, they decide to get Donald back as their leader by pretending to have glitches in their bionics to humiliate Graham in front of the President of the United States when he comes to visit them. In the end, Donald is back as their leader after Agent Graham is fired by the president, arrested by the Secret Service, and sent to prison.

Donald and the Lab Rats attend a fan convention about the movie, Alien Gladiators. The Lab Rats queue up to meet Andre Ethier, but Caitlin comes and makes them let her cut in line in front of them, getting the lost spot and meeting Andre Ethier. They fight with Caitlin and are thrown in a security holding area with a fanboy. Meanwhile, Leo and Donald are taking part in the Fire Staff Competition to get the walk-in role in the next Alien Gladiators movie.

Chase feels that it is unfair to be picked on by Adam every time and tells Donald. Douglas overhears and unlocks a new ability for Chase, upsetting the balance in the house. Douglas tries to fix things by giving Adam a new ability as well, but Adam and Chase end up fighting with one another. Meanwhile, Bree tells Leo about a contest at Tech Town as they are about to hit their one-millionth customer and Leo competes to ride on the first anti-gravity roller coaster and meet the owner of Tech Town. Principal Perry tries to compete to crush Leo's dream. In the end, Chase and Adam have a death battle, but eventually forgive each other and find out that Douglas gave Bree the ability to go invisible, scaring everyone in the lab.

Chase gets a girl interested in him, but Adam gets jealous and tries to ruin their date by having Chase turn back into Spike. Meanwhile, Leo and Bree suspect that Principal Perry has murdered a cook from the cafeteria and Donald. They then find out it was about a hamburger truck and they misunderstood everything.

Bree wants to get revenge on Adam for embarrassing her in front of her boyfriend, Jake. Working with Chase, she puts on a cyber cloak that makes her look and sound exactly like Principal Perry and embarrasses Adam in front of the whole school. However, when she shows Adam the cyber cloak right before the dance that night, it glitches and won't come off. Bree then makes Chase wear a cyber cloak of herself and go to the dance with Jake. While that's going on, Leo and Douglas snoop in Donald's briefcase and compete for what they think is to be his new vice-president, only to find out it was for the Davenport Industries softball team. Donald then finds out that he had two cyber cloaks missing and deactivates them. This embarrasses Chase and gets Bree into trouble with Jake. She then thinks she's patched things up with Jake, but it's really Principal Perry wearing a cyber cloak.

During Christmas, when the Lab Rats discover that their new action figures are being outsold by another toy, The Nerble, they attempt to improve their toys by adding special features. After adding them they decide that the toys are too dangerous for kids and put them in a box to be destroyed. Tasha is running a toy drive at the school and is collecting gifts. She finds the action figures and hands them out. When the Lab Rats find out, they rush to school and try to catch the action figures. After destroying the toy drive, they find a way to make it up to Tasha and the kids. Leo and Donald have a snowball fight in the house and Grandma Rose shows up just as Leo uses his bionic arm. Rose gets mad and calls Donald a bad father. Donald tries to makes it up to Rose by giving her a Bree action figure, but it promptly explodes.

The Lab Rats plan to gain good publicity by having cameramen film them during a mission, but it turns into a disaster when they fight for screen time. After the mission, the president orders the team to stay away from the public in order to let him settle things down. However, it goes wrong when Leo and Principal Perry are holding back angry protesters who want the Lab Rats gone, and Leo accidentally uses his bionic arm. As the protesters become even more enraged, they try to storm the house; Adam panics and uses his bionic super breath to blow everyone off the premises. However, Chase criticizes Adam's actions and the Lab Rats start fighting. They eventually decide to break the team. Three weeks later, the Lab Rats refuse to talk to each other, but they are forced into action when Krane plans to use his Triton App on everyone in the world. A large battle ensues, pitting Leo, Donald, Douglas, and the Lab Rats against Krane and his bionic army. Most of the soldiers attack Adam and Bree, who manage to take them out. Chase has a one-on-one battle with S-3 and Leo has one-on-one battle against S-1. Donald and Douglas attack the soldiers surrounding the satellite, but Krane keeps them from getting too close. Eventually, the Lab Rats and the rest of the team manage to hold back many of the soldiers, but they are running out of time to stop Krane. Douglas then reveals that the Lab Rats can fuse their abilities to stop Krane. They succeed, blasting Krane into the sky and breaking his control over the soldiers. However, their victory is cut short when they find out that Donald is in serious condition after the battle. Later they find out that after the surgery, Donald is still in a very delicate condition. Leo is made an official member of the Lab Rats and gets an upgrade to his bionic arm.

The Lab Rats plan to gain good publicity by having cameramen film them during a mission, but it turns into a disaster when they fight for screen time. After the mission, the president orders the team to stay away from the public in order to let him settle things down. However, it goes wrong when Leo and Principal Perry are holding back angry protesters who want the Lab Rats gone, and Leo accidentally uses his bionic arm. As the protesters become even more enraged, they try to storm the house; Adam panics and uses his bionic super breath to blow everyone off the premises. However, Chase criticizes Adam's actions and the Lab Rats start fighting. They eventually decide to break the team. Three weeks later, the Lab Rats refuse to talk to each other, but they are forced into action when Krane plans to use his Triton App on everyone in the world. A large battle ensues, pitting Leo, Donald, Douglas, and the Lab Rats against Krane and his bionic army. Most of the soldiers attack Adam and Bree, who manage to take them out. Chase has a one-on-one battle with S-3 and Leo has one-on-one battle against S-1. Donald and Douglas attack the soldiers surrounding the satellite, but Krane keeps them from getting too close. Eventually, the Lab Rats and the rest of the team manage to hold back many of the soldiers, but they are running out of time to stop Krane. Douglas then reveals that the Lab Rats can fuse their abilities to stop Krane. They succeed, blasting Krane into the sky and breaking his control over the soldiers. However, their victory is cut short when they find out that Donald is in serious condition after the battle. Later they find out that after the surgery, Donald is still in a very delicate condition. Leo is made an official member of the Lab Rats and gets an upgrade to his bionic arm.

Donald is in critical condition after the battle with Krane and his soldiers; Leo visits him in the hospital and in an attempt to save him, he risks his life to perform a dangerous bionic process, accelerating his aging process, thus turning him into an old man. Meanwhile, after being deactivated from the Triton App, Krane’s former bionic soldiers have nowhere to go and follow Adam home. The Lab Rats try to protect them because they aren't evil anymore. However, the president doesn't get this and tries to have them arrested, but changes his mind when the soldiers use their powers to heal and save Leo who almost died of old age. Right when they are going to be taken into custody, a newly healed Donald strikes up a deal with the president to build an academy for the soldiers.

Leo finds out that he will be a student at the bionic academy, not a mentor like Adam, Bree and Chase. Chase engages in a battle against a former nemesis and Adam mentors a younger student.

Donald leaves the Lab Rats in charge of the bionic academy while he celebrates his anniversary with Tasha. Leo invites Janelle to the island, but gets distracted by his nemesis, Spin. Spin challenges Leo to a bionic battle. Meanwhile, Adam tells Bob to do all the things he can't do when Donald is around. Bob goes ahead and steals Donald's plane, but he then hits a button that deactivates the auto-pilot. Sebastian and the Lab Rats work together to save Bob. Back at the bionic battle, Leo tries to impress Janelle by battling with Spin. Spin gets the first attack and knocks Leo over. Leo then fights back and hits Spin in the leg. Janelle rushes over to Spin, who is crying, and helps him up. Janelle gets upset at Leo and takes Spin to get a smoothie. It is then revealed that Spin faked the injury so Janelle would spend time with him. Leo tries to prove that Spin is faking it by taking his crutches. Janelle then yells at Leo and carries Spin away. Leo tries again by filming Spin admitting faking the injury, but Spin then smashes Leo's tablet. Janelle walks in and yells at Leo and Spin. Leo and Spin then become her servants and they must give her the vacation that she deserves. Later, Adam uses Donald's jet wing to fly up to the jet and save Bob. When Adam tries re-activating the auto-pilot, the plane begins to fall. Adam helps Bob conquer his fear of heights by jumping out of the jet. Bob takes Adam's parachute and Adam jumps out to try to get it from Bob. At Donald's house, just as Donald finishes setting up the table, Adam and Bob fall through the ceiling. Donald is disappointed with the Lab Rats. Adam confesses and tells him that he wasn't a good mentor. Bob tells Donald that Adam was a good mentor by boosting his confidence. Donald then tells him that his plane was a smart plane that even without the auto-pilot the plane would land itself automatically.