Lee is chased around Landmark City by Dragon. He ends up in his office in Lee Industries and erases all files on Mu-Team from his computer. Dragon is after those files, so he fights Lee. Lee falls off the roof of the building, his hardlight armor saves him from the fall but his body starts to absorb hardlight. The process is irreversible. Lee also goes back 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 Tale 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 Tale sent Dragon to find Lee. Lee regrets his actions, Axel leaves to find The Serpent's Tale leader, who is revealed to be Kuan. Kuan finishes off Lee and attacks the aquatic center. Axel and Kuan fight, Dragon tries to protect Axel, a large explosion from one of the attack's leads to the building being about to corrupt. Kuan and other his henchmen escape but alpha teens can't get out. Lee appears in a form of a ghost made of 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. The team and Dragon are safe, Lee disappeared, and Kuan, back in his headquarters, says that the fight isn't over yet.

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 Paine, Spydah and Flesh are arrested, Lee fires the Alpha Teens, strips them all of access to their vehicles and their credit line. As the five are forced to get normal jobs, Axel is attacked by Lee’s creature.

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.

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.

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

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.

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.

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.

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

Lee reveals to Axel that his creature, Tilian is Axel’s mutated clone. He tells Axel his true intentions which gets him stripped of all his power at Lee Industries. Lee experiments on himself so he could be super-intelligent and super-strong, but the Alpha Teens stop this and Lee becomes completely evil. Lee hints to a Mu-Team and that Tilian isn't his only clone. Also still finding work, Shark and Hawk compete as ice cream men.

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.

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!

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.

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

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.

The team encounters a new foe, nicknamed "The Racer." His reason for being? Stealing one-of-a-kind vehicles! (The whole episode plays like an episode of some reality television program.)

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

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. Lee captures Dragon and creates a cybernetic clone with which to destroy Axel.

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

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 dad, 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.

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.

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, the later investigate a mysterious dream Axel had of his father claiming "Jo-Lan" is in danger.