A council of seven supervillains is formed, eventually agreeing on The Elite as their name. But, who is the inside man that one of the members of the Elite says he is? Meanwhile, 5 Magisters debate the idea of bringing a new class of recruits to the Plumbers' Academy. Then, Magister Lotin returns and they discover that major super villains have escaped from Incarcecon. They head to investigate and discover a break out in progress, but is it just a diversion so another villain can destroy the academy?
The 6 Magisters find themselves trapped in their own academy by a network of evil plants. They find Dark Viper, who only re-traps them in the plants and sets a timer that will detonate explosives in one hour. She leaves, but not before telling the Magisters that the break out wasn't a diversion and that there is a mole among them. Can they find out who the mole is a disable the explosives in time? Meanwhile, Chemestris breaks out all the prisoners in Incarcecon after revealing she disquised herself as Magister Baren; Blitz and Lucifer head to Ranova to set up a base.
When Plumber recruits head to the Academy to begin their training, the are immediately plunged into a situation where they find Vilgax attacking the Academy. Despite the Magisters and other Plumbers warning them to stay in their barracks, can they stop Vilgax from destroying the Academy before their first day of class?
When Zon sneaks into a room with dangerous weapons, he gets affected by a machine that makes him randomly switch between aliens. At the same time, the other members of the team get kidnapped by Dr. Animo. Can Zon use his messed up powers to save his teammates?
After a successful first day of classes the gang decides to go snooping around the Academy to see if they can find out any "cool" information. When Paper discovers a secret stash of files and an entire complex underneath the academy, can he escape Lotin and figure out why he is acting so strangely, while at the same time securing the files?
After another successful day of classes, the recruits get told they will have no classes on the weekend. The next day, they decide to introduce themselves to the other students at the academy, but they get into a fight with a student named Crash. Can they defend themselves from Crash?
After a new recruit named Rex arrives at the Academy, the original Cadets think that he is just a spy working for the Elite. Can they convince him to stop spying on them and join them for real, if he is even a real spy?
Rex officially joins the Team. Everyone hangs with him, apart from Paper, still thinking he's an evil spy working with the Elite. Then, the Magisters ban Rex from the Plumbers' Academy. As soon as Rex controls the minds of the recruits, Paper finds out that Rex was rejected from PA because of going evil; does Paper have enough time to save his friends, along with the Academy?
After Ben Tennyson visits all the students of the Academy, the recruits decide to see if they can get any information about the Elite from him. Can they save Ben from who ever is trying to eliminate him without letting him know they are secretly following him for information?
The recruits discover the exsistence of a bounty hunter named Ra'ol Set who has been hired by an unknown force to eliminate the Elite. With the team wondering who is the villain in this scenario, can they make the right decision and defeat the true evil?
The recruits get assinged to each do a report on one of the biggest battles in history, but when one of Ben's old foes comes to the Academy looking to destory it, they have to put their report on hold to stop him. Can they stop the villain and finish their reports?
When Water suddenly disappears, the recruits have no idea where he is. They then find that their files have been hacked, stolen, and erased. They decide that the files were taken by Water. Feeling betrayed they go to look for him. Elsewhere, Water is having a secret meeting. Can the find out if Water did what they think, or is someone else behind the whole thing?
The gang gets caught sneaking around the Academy by a Magister and gets sentenced to detention. During the detention, they notice that every Magister has left the building on a secret mission except for the one stopping them from leaving their barracks. Can they escape the barracks and stop an unknown threat from taking over the Academy while the Magisters are away?
After figuring out that Lotin wanted them to figure out he was the mole in order to confuse them when Ra'ol Set attacked, the recruits confront Lotin and break his control over the other Magisters. Lotin flees, giving the recruits time to fill the freed Magisters on what has happened over the last few months and allowing the Magisters to give the recruits the backstory on Lotin, but soon enough, Lotin returns with Aggregor and attacks the academy? Can they stop Aggregor and Lotin and figure out who the members of the Elite are?
When a mysterious enemy comes to the Academy, the recruits start disappearing. Eventually, the recruits figure out that the recruits are being abducted by aliens and the remaining recruits try to stop the threat. When Paper finds himself alone, can he convince his alien doppelganger Pencil to betray his fellow invaders and help him find his friends?
When the gang has to take the written portion of their first test, Brian and Jack get caught cheating, so they decide to go around the academy snooping for secrets about the gang. They break into Rob and Sci's lockers and find what they were hiding from the rest of the gang. They encounter Paper, who was the first to finish (becuase of his accelerated brian) and try to explain what they were doing. Can Paper stop them from getting Rob and Sci expelled because of their secrets?
The recruits prepare for their field exam: a full mission to the planet Vrellax and rescue a bunch of hostages and then defeat the "villains" that are the Magisters. On their way to Vrellax, the recruits are ambushed by Lotin and a fleet of starships. They are shot down to the nearby planet of Viscosia, Goop's home planet. Can they find a way off the planet and escape Lotin's fleet in this process? Meanwhile, wondering where the recruits have gone, the Magisters return to the Plumbers' Academy and find it under attack by Ra'ol Set and Lucifer. Can they save the academy from two of the possible members of the Elite?