After competing in and completing the reality show, Trackdown, the five contestants, Axel, Hawk, King, Lioness and Shark are offered jobs to test new and experimental vehicles for Mr Lee, Trackdown’s creator and president and founder of Lee Industries, a multi-billion dollar company. The five accept his offer, but when a dangerous criminal mastermind named Alexander Paine escapes from prison, Axel has personal interest in helping recapture him.

Lee, who is acting clingy and parental around the team, equips them with new gear and weaponry to test. At the same time Paine and his henchman Spydah seek to destroy the Landmark City dam. Axel also tells Lioness about his past with Paine.

The Alpha Teens move out of Lee’s R & D physicality and into an abandoned Aquatic Center. Meanwhile, due to a freak accident caused by Axel previously, Paine gains new powers that emit terrible pain through his body which he can transfer to those he touches. With these powers, Spydah and added help from the acrobatic Cannonball Bros., Paine goes to Lee Industries, seeking revenge on Axel Manning.

Paine learns of Nutronium, a chemical that can put an end to his constant pain. He and Spydah seek to steal it with the help of Albert, a dangerous muscle-laden criminal who uses a barbell for a weapon. In the heat of battle with the Alpha Teens, Paine unintentionally mutates Albert into the super-strong giant, Flesh.

The Alpha Teens, Lee and the building security board head of Landmark City become trapped in the yet to be opened Lee Plaza. The culprit, Silas Greene, the building’s deranged architect, seeks revenge against Lee by using the building’s security robots and other lethal functions to dispose of him.

The Alpha Teens accompany Hawk, who stars in the movie being filmed, "Radioactive Island", to an island that served as a military testing site. While King’s animalistic nature unintentionally steals Hawk’s thunder, it also gets the attention of Recombo, a mad scientist who combines different species of animals into one.

When Shark skips out on a fancy party held by Lee on his yacht, he is captured by the villain, Doctor Eel. With various sea creatures under his mind-control, Eel sends his "pet" giant squids to sink Lee’s yacht.

At Christmas time, while the other Alpha Teen members are packing to visit their families, a lonely Axel thinks of his late father, Sebastian. He is attacked by Dragon, a ninja mercenary, who like Axel, is skilled in the Jo-Lan martial arts.

Bogey, a rival of Hawk’s, gets under Hawk’s skin at an airshow. Later, Hawk and the other Alpha Teens are trained to fly Mr. Lee’s Hypersonic Stratojet, an aircraft Paine has every intention on stealing.

On their way to the frosty Iron Mountain, the Alpha Teens are greeted by Dr. Magness, a doctor at a ski resort. After a wired rash of incidents involving the team’s vehicles, including a car crash that injured Lioness’s leg, she suspects that there is more to Dr. Magness than her teammates realize.

As Paine plots to steal plutonium from Landmark City’s nuclear power plant, Col. Richter of Landmark City’s law enforcement thinks (with very strong video evidence) that Axel stole an armored car filled with money. At the same time, Axel’s father, Sebastian Manning, seems to be alive.

Paine steals cyborgs from one of Lee’s factories. Having Spydah duplicate their schematics and create more, Paine now controls his own cyborg army.

Paine unleashes a huge hurricane on Landmark City with the Atmospheric Modifier, a device made by Dr. Nimbus, whose family Paine is holding hostage.

King has his eyes set on winning the WWC World Title Belt under the guise as the wrestler Royal Rumble. Paine however, seeks the belt for his own dastardly schemes and hires the rhyming extortionist, Vinnie Rossi to stand in for an injured Flesh. During the WWC battle royal for the title, Vinnie’s lovesickness for Lioness could cost him the match and much more.

Lee introduces the Alpha Teens to the somewhat insecure teenage genius, Garrett. In another scheme to ease his own inner pain, Paine sends Flesh and Spydah to kidnap Dr. Evans, an expert in sound wave research and Garrett’s former professor at Landmark University.

After Spydah is fired by Paine for failing to get a crucial flash drive that was protected by the Alpha Teens, he intends to prove himself to his former boss.

After Lee’s Mecha Speeder and the crew of the cargo ship that held the vehicle go missing, the Alpha Teens are sent to investigate on Halloween night. What they find is a virtually lost portion of Landmark City filled with zombies. Their leader, Bonez, soon makes Hawk, Shark and Lioness part of their ranks.

After being stopped by the Alpha Teens once again, Paine enlists the aid of five extreme athletes to take them out once and for all.

Magness returns to Landmark City with her new biker boyfriend, D-Zel. She systematically causes problems for Landmark City, the Alpha Teens and her father, Paine. D-Zel experiences a change that makes him truly one with his bike.

When a corrupt cop falsely accuses the Alpha Teens of grand theft auto, they become fugitives of the law. Worse yet, Hawk and King are captured, arrested and sentenced to serve time in the same prison where some of the villains they busted were sent to.

After a meteorite temporarily knocks out all power within Landmark City, Paine intends to steal it to make the city go through a much more permanent blackout. Also, Hawk poses as the leader of the Alpha Teens so he could impress reporter, Michelle Moreno.

Flesh and Spydah poison Axel with potent venom from a very toxic water spider. As Axel, who is using Jo-Lan to slow down the toxin’s deadly effects, is getting medical attention, Shark is put in charge of the team by Axel himself.

The mystical sword of Jo-Lan is stolen from the Landmark City museum by a group of ninjas and the Alpha Teens go all the way to Hong Kong to recover it. Dragon returns with interest in the sword, mysterious intentions and unsure alliances.

As the Alpha Teens finally discover where Paine’s base is located, Paine seeks to tunnel under Landmark City flood the city with lava. However, because of the intense heat of the lava, Paine forces Vinnie Rossi, now the monstrous concrete man, Mass, to do the job, or else his mother will pay the price.

Now, without a base to call home, Paine seeks to use a remote that can control electronic devices to blackmail Landmark City into giving him enough money to rebuild. Lioness's cousin from Brazil, Eliza comes to visit and immediately has Hawk and Shark attracted to her. Axel and Garrett stumble into a mysterious room of Lee Industries that is off limits to anyone but Lee himself.

Ten years at the day since the potential death of his father due to a bomb created by Paine, a frustrated Axel seeks to put Paine out of commission for good, even if it means interfering with police business and splitting up the team. Meanwhile, Lee creates a lizard-like creature called the "Axel Manning advanced enhancement".

The Alpha Teens are fired from their jobs with Lee and kicked out of their home! Faced with the prospect of "real jobs" and the prospect of being homeless, things get worse when a strange hybrid creature named Tilian comes after Axel, intent on killing him. Will the gang find a new home? Will Axel survive? And just what does Mr Lee have to do with Tilian?

Lee reveals to Axel that his creature, Tilian, is Axel’s mutated clone. He tells Axel his true intentions which subsequently gets him stripped of all his power at Lee Industries. Lee then experiments on himself in order to become super-intelligent and super-strong, but the Alpha Teens ruin this experiment – thus, Lee went completely insane. Lee mentions a Mu-Team and that Tilian isn't his only clone. Also still finding work, Shark and Hawk compete as ice cream men.

With the Aquatic Center totaled by Paine, Spydah and Tilian collectively, and still trying to find paying jobs, the Alpha Teens make a rundown apartment their new home. Garrett, though may have a solution to their problem. Meanwhile, Lee sends mutant clones of Lioness and King, Firekat and Wrecka respectively, to destroy the team.

Shark lands a job as a lifeguard where he meets a beautiful scientist named Dr. Rachel Logan and they take instant liking of each other. Unfortunately Mr. Lee has Rayza, Shark’s mutant clone, kidnap Rachel. Hawk is taught the basics of swimming as he and the other members of the Alpha Teens are attacked by his mutant clone, Stingfly.

Lioness is asked to give a public speech at a fundraiser, bringing to the surface her old fears. Lee lures Axel into a trap and sends the Mu-Team, including a thought-to-be-dead Tilian, to capture him.

Needing a bit of extra intelligence to correct a design flaw (with Hard Light), Mr. Lee takes over the advanced school where King's brother, Duke, attends. The process in which Lee uses to siphon all the students' intelligence into Duke turns him evil and gives him telekinesis.

King takes the team camping in Blue Pines National Park for his birthday. The park, however, has become nothing as King described it. A vicious mutant, combined of different animals, is loose in the park.

Paine receives a letter with a photo of himself, Axel's father and some other people who are crossed out and he also receives a disk from which he is very scared. He wants Axel to guard him and he promises to tell him about his father. Dragon and an army of ninjas kidnap Paine and Axel and his friends go to save him. When they rescue Paine and put him back in jail he gives Axel a picture of his father and a man whose face is burned from the picture. Paine tells Axel that when he finds the person on the picture he will find his answers.

A new airplane is created by a friend of Garrett. However Garrett does not trust him, so Axel is told to check out the plane. When Garrett's friend spots him he is forced to leave. Then the Mu-team arrive to steal the plane, but Axel, Lioness, Shark, King and Hawk stop them. The Mu-team then smash a building and Shark saves the building but gets zapped by an electrical wire and becomes unconscious, meanwhile the Mu-team steal the airplane. When Shark awakens he believes himself to be a military person. The team are told to listen to Shark or he may sustain brain damage. Later the Mu-team uses the airplane to steal an experimental liquid, and Tilian drinks it, making him grow into a giant, but the team defeats them and Shark is returned to normal.

After Mr. Lee breaks Recombo out of prison, Recombo invades the dreams of the A.T.O.M. team.

Lioness' neglectful rocker father comes to visit, hoping to mend fences with his daughter. Meanwhile, Magness is planning a major heist – at the very concert the team is attending!

While searching through Mr. Lee's soon-to-be destroyed mansion, Axel discovers a canister with a map written by his father, directing him to his hometown. Meanwhile, Lee captures Dragon and creates his cybernetic clone in order to destroy Axel once and for all.

During a call to Lioness, her cousin Eliza is attacked and kidnapped. The team travels to Brazil to rescue her.

During the holiday season, King volunteers to be Santa at the local mall, Lioness as Mrs Claus with the others as his elves. The toys they give out, however, are not what they seem – Lee has added his "special" creative touch.

When Rachel's marine biologist father, his boat, and his crew go missing after coming across the mysterious Kraken, it is up to the team to help her. Things only point to Lee as Rayza makes an appearance.

Vinnie "The Mass" Rossi returns – now as molten magma man – bringing freak volcanic rifts all over the city. The reason behind his appearance? Lioness. On a side note, the extremeness of Hawk and Shark's snow fun causes $97 million in damages, which the city expects the two to pay.

Lee and the Mu-Team take over the space station while Garrett is aboard making final adjustments. Able to send a message to the team, he asks for help. With no other options, the team "borrows" the still-experimental Cosmo Jet and gets spacebound.

Axel tries to figure out what happened to his father, using everything he can remember to unlock the codes and his dad's files. Dragon appears out of the blue and engages Axel in a fight. Axel knocks him to the ground and removes his mask only to see... Sebastian Manning! In the end, it is revealed that the government was trying to clone a super-human, and all clones were marked with tattoos on their chests. Dragon removes his shirt to find that there is a tattoo on his chest, while Axel is devastated. As a side story, Hawk's ex-actor father drops in for a visit.

Lured to a remote island with a recorded audio loop of Axel's father, the team falls into the trap of a demented game hunter, who considers them to be the ultimate prey.

A peaceful day at the city zoo for Axel, King, and Shark turns into another fight with Lee and the Mu-Team when the latter are there to use the zoo's newly acquired Hybridon (the mutant amalgam of animals responsible for the previous closing of Blue Pines National Park) for nefarious purposes. Meanwhile Hawk needs Lioness help to get a girl from her capoeira class but it does not turn out to smoothly as she is a nutter.

Wanting to prove himself to Lee and the Mu-Team, Wrecka goes to steal a shipment of Thurlium – increasing genetic mutations fivefold – alone. The only team member at home, Hawk is sent by Garrett to stop him. Problems arise when both are captured by Magness, who wants the Thirlium to increase her own magnetic powers, and they must work together to stop her.

After taking a page from the always-bickering Mu-Team, Lee sets out to break apart the Alpha Teens by setting them up to distrust one another and fight amongst themselves.

The team encounters a new foe, nicknamed "The Racer". His reason for being? Stealing one-of-a-kind vehicles!

Note: The whole episode plays like an episode of some reality television program.

Hawk is given a part in a Kung-Fu movie in Hong Kong, but gets in over his head. As the other Alpha Teens come with him, they later investigate a mysterious dream Axel had of his father claiming that "Jo-Lan" is in danger.

The Alpha Teens find Mr. Lee's hideout and come face to face with a Mu-Team who are growing tired of their creator.

Lee is chased around Landmark City by Dragon. He ends up in his office in Lee Industries and erases all of the files on the Mu-Team from his computer. Dragon is after those files, so he fights Lee. Lee falls off the roof of the building, his hard light armor saves him from the fall but his body starts to absorb the hard light. The process is irreversible. Lee also reverts to his "old self". Axel comes to Lee Industries, and Lee tells him that Dragon was Sebastian's clone he had created. Sebastian and Lee were friends, but Lee needed more money for his experiments, so he took it from the Serpent's Tail in exchange for government cloning secrets. Manning caught him and wanted to expose everything, so the Serpent's Tale took him out to protect their money. After that Lee didn't want anything more to do with them, so he quit the project, but the Serpent's Tail sent Dragon to find Lee. Lee regrets his actions, Axel leaves to find The Serpent's Tale leader, who is revealed to be Quan. Quan finishes off Lee and attacks the aquatic center. Axel and Quan fight, Dragon tries to protect Axel, a large explosion from one of the attack's leads to the building being about to corrupt. Quan and his other henchmen escape but the Alpha Teens can't get out. Lee appears as a ghost made of hard light and says that "science has given him a means to make amends for all he has done starting now". He teleports the teens and Dragon out of the building which then explodes.