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 make Hawk, Shark and Lioness part of their ranks.

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.

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

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.

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 using the building’s security robots and other lethal functions to dispose of him.

A year after 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. Lee creates a lizard-like creature called the "Axel Manning advanced enhancement".

Shark lands a job as a lifeguard where he meets a beautiful scientist named Rachel. 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 clone, Stingfly.

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 Paine escapes from prison, Axel has personal interest into helping recapture him.

As Paine plots to steal plutonium from Landmark City’s nuclear power plant, Col. Richter of Landmark City’s law enforcement accuses (with 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 unleashes a huge hurricane on Landmark City with the Atmospheric Modifier, a device made by Dr. Nimbus, whose family Paine is holding hostage.

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.

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 has a solution for their problem. Meanwhile, Lee sends mutant clones of Lioness and King, Firekat and Wrecka respectively to destroy the team.

Vinnie "The Mass" Rossi returns -- now a 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, 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 touch. 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.

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.

When Mr. Lee breaks Recombo out of prison, he (Recombo) invades the dreams of the A.T.O.M. team.

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 steals Hawk’s thunder, it also gets the attention of Recombo, a mad scientist who combines different species of animals into one.

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.

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 aeroplane. 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 aeroplane to steal an experimental liquid, and Tilian drinks it making him grow into a giant, but the team defeat them and shark is returned back to normal.

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!

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