The next year, the only recruits left are Paper, Aevan, Ben, Jack, Zon, Toon, and Brian (Bink, Sci, Rob, and Water are gone/missing). With no major problems surfacing lately, the team is shocked to intercept a secret transmission from an alien planet to the UN Building on Earth telling them that an invasion is coming. When they decode the message, they discover it was sent from Salimore, a planet notorious for its bounty hunters, including Ra'ol Set. Can the team go to Salimore and destroy the invasion force before it can launch, and also find out more about the mysterious Elite that disappeared without seeming to be defeated?
After the time skip in the previous episode, it is already January 2014 and new recruits have arrived during the time while they were gone. They meet the new recruits and give them a tour, but then the academy gets attacked by the Highbreed and DNAliens. Can they stop this seemingly random attack and prevent the veteran recruits from being captured?
Rex and Rocket, along with their new partner Ancy, come to the Academy and suggest a competition between the recruits of the Plumber's Academy and the recruits of the Villain's Academy. Can the Plumber's newest recruits win while the veteran recruits search the villains academy for clues as to where the Elite has gone to?
Paper takes a team of the new recruits to an ice planet where they find a secret meeting of crime lords from different ice planets around the galaxy. They discover that the group, known as the Glace (the french word for ice), has recently acquired a weapon of mass destruction from what is most likely the Elite. Can the recruits take the weapon without the Glace noticing and discover what it is for, and more importantly why they acquired it?
A virus infection plagues the recruits and stops them from going out on a mission. During this time, only the people who are not sick, being Brian, Aevan, Toon, Zon, and two of the new recruits try to search for a cure while stopping Chemestris who is trying to prevent them from doing this. Can they apprehend the doctor and get the cure in time?
The recruits discover the existence of a fighting ring on the planet Hitalbur. The winner is said to get a belt the houses the "finest crystal you will ever see." While Sub, Nick, and Will rise up in the ranks in the arena, Toon, Zon, Brian Nar, and Cassie check out the facilities to see if anything is more than what meets the eye. Can both teams succeed in their goals while Paper tries to prevent the defending champion from figuring out what is going on?
The recruits discover that the Forever Knights have been running illegal trade operations back on Earth. All the recruits head their and sneak into the Knight's base where they find a portal to the Null Void so that the Knights can quickly reach the far side of the galaxy for easy trade. Once in the Null Void, the new recruits discover that a powerful creature has escaped and is trying to find the power source guarded within the depths of the void to fully reform himself. Can the new recruits get the power source before the creature does while the old recruits stop King Arthur from closing the portal.
Crossover: Having discovered the Elite's alliance with Alpha and their plan to destroy the Galactic Business Association, they head to the HQ of the GBA to stop a planned attack. Elsewhere, an ancient demon sorcerer steals a mirror from a vault and then accidentally triggers the copies of the mirrors in other dimensions to be activated, pulling in the greatest heroes from 8 other dimensions. Eventually, Virton meets up with the Elite and the heroes meet, but can they stop the Elite and their plans with the mirror, in addition to defeating Virton and Alpha?
With three crystals in possession of the Elite, the recruits break up into four teams: one to stay at the academy, one to go to the Villain's Academy, one to go to Salimore, and one to go to Ranova, where each of the crystal are being held. While most of the recruits are off, the remaining recruits and the Magisters defend the Plumbers' Academy from King Arthur, Doctor Blitz, and Chemestris. With each of the three bases having another member of the Elite, Lucifer at the Villain's Academy, Viper on Ranova and Ra'ol Set on Salimore, the question remains as to where Lotin is. Can the recruits find the three crystals, keep their crystal safe, and defeat the Elite once and for all?
Having lost gotten two of the three crystals from the Elite and still having theirs, the Magisters and most of the recruits head to the Temple of Rigon to gain the power for themselves. Meanwhile, Toon, Ben, Will, Sub, and Cassie head to an empty ChemiLabs to find the real Water, Rob, and Bink. Can both groups complete their tasks or will the Elite come out on top?