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.

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.

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 whos 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 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.

When Mr. Lee breaks Recombo out of prison, he (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!

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

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.