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Raiders of the Lost Arkus, Part 2 is the thirteenth and final episode of Skylanders Academy Season 3. It also serves as the series finale.
Kaos and Glumshanks mount the Arkeyan Conquertron and refuses to listen to Strykore or Kaossandra, as he fully intends to destroy the Core of Light. Master Eon urges the Skylanders to prevent Kaos from making it to the Core of Light, but Strykore blasts them all off the island's terrain, sending them downwards. Luckily, Captain Flynn, though unaware, manages to catch them with the Dread Yacht. The team realizes their combined strength alone is not enough to stop the Arkeyan Conquertron, and with the Academy too far away, Spyro suggests they seek help from the Wumpa Islands. Master Eon and Kaossandra are left to confront Strykore. With Kaossandra powerless, Eon decides to transfer a significant portion of his powers to Kaossandra, despite her concern that it would weaken him. All three powerful mages use their magical energies as they engage each other.
Meanwhile, the Doom Raiders enjoy their time relaxing at the pirate ship celebrating the removal of their former pirate captain, oblivious from the Arkeyan Conquertron rising from behind as Kaos angrily watches and overhears the Doom Raiders ridiculing him. As a final goodbye to his pirating days, he uses the giant robot's arm to violently swat the pirate ship, hurling it far away. Kaos continues on to the Citadel, and finally makes it to the Core of Light. However, he is halted by the presence of the Skylanders, reinforced by Crash Bandicoot and his tech-genius sister, Coco.
Master Eon and Kaossandra continue to battle Strykore, but he is able to defend himself against every magic spell they throw. Eventually, it becomes a duel of brother against brother, as Kaossandra is outmatched. Strykore tries to get Eon to act merciful, recalling how close they used to be. Kaossandra tries to dissuade Eon, reminding him that Strykore destroyed their brotherhood once he turned evil. But this proves enough for Strykore to gain the upper hand and manages to overcome Eon, who falls unconscious. Fortunately, Kaossandra manages to overpower Strykore, releasing her anger for what he did to Kaos. Strykore then tries to persuade her to join his side of evil again, even offering her a position to rule the Skylands with him, making Kaossandra pause.
The Skylanders exert all their efforts in attacking the impenetrable Arkeyan Conquertron, frustrating Kaos as they keep blocking his chance to get near the Core of Light. To ward them off, Kaos uses the Iron Fist to summon two smaller but powerful arkeyan robot minions to deal with the Skylanders. With his path clear, Kaos prepares to smash the Core of Light but is halted by Glumshanks, desperately trying to hold on to Kaos's arm in an effort to save it. Kaos realizes his loyal friend is following her mother's wishes, and so he tries his best to remove the troll's arm but Glumshanks relentlessly clings on.
Kaossandra is pressured by Strykore's offers as he promises her that once she joins him, she would once again have Kaos by her side and never have to learn the real truth about his origins. Kaossandra refuses to let Kaos live his life a lie and denies Strykore. Their conversation allows Eon to regain consciousness in time to summon a portal, where Kaossandra strikes Strykore hard enough to get him dragged back into his dimensional prison. Eon and Kaossandra reunite their powers and closes the dimension, hopefully ending Strykore's threat to the Skylands. After the fight, Eon is heavily weakened but he and Kaossandra fortunately picked up by Captain Flynn to take them to the Citadel.
Despite their best attempts, the Skylanders are outmatched by the Arkeyan robots. Coco finally manages to ready her Electromagnetic Pulse Cannon and, despite the risk it could backfire, uses it against the Arkeyan robots that it completely shuts their systems down. Pop Fizz attempts to fend off the Arkeyan Conquertron by throwing Coco's boomerang but misses Kaos entirely. Kaos eventually manages to regain control by pushing off Glumshanks. But he is halted once again, by the arrival of Kaossandra and Master Eon, pleading for her son to stop. Kaos has no intention of listening to his disowned mother, so Eon instead asks he listen to his father, which he reveals is actually him not Strykore, much to the surprise of the Skylanders. But Kaos takes a long time to process his revelation, so Eon clarifies it by revealing again the same symbolic mark he bears in his forehead, which Kaos also recognizes, finally realizing the awful truth.
Master Eon explains that he and Kaossandra tried to keep his identity a secret, since Kaos was at great risk from being abducted by villains as his parents are both the most powerful mages in the Skylands. With this, Eon tells his son that (in addition to being able to grow a beard) he is capable of being benevolent. But Kaos refuses to believe he has good in himself, not willing to give up his evil nature. But all of the Skylanders believe he can be good, as Spyro relives his moments with a kind-hearted Kaos when he ended up at an alternate timeline. Kaos pauses as everyone waits if he would finally make the right decision. But before he can choose, the boomerang thrown earlier hits the Iron Fist causing Kaos to tip the Arkeyan Conquertron, aiming at the Core of Light. Without a moment's hesitation, Eon uses the last of his strength to summon a powerful magical blockade that causes the Arkeyan Conquertron to vanish, saving the Core of Light and Kaos, to everyone's relief. But in the process, the Skylanders notice that Eon is missing, with his helmet being the only remains, leaving Kaossandra to conclude Eon sacrificed himself.
Despite the salvation of the Skylands, the Skylanders make their way back to the Academy with a heavy heart. Kaossandra breaks the silence, unable to keep it further, she reveals that Eon gave a great deal of his powers to Kaossandra and without enough time to replenish his strength, the powerful light spell Eon created to save the Core of Light was at the cost of his life. The team gathers around her, as Stealth Elf contemplates the future of the Academy. Stealth Elf concludes that there is no one else more worthy to fill in and carry on Eon's position at the Academy than Kaossandra, to which she accepts the honor, with her first act being to elevate the team's ranks as Skylanders, where they have the honor to teach the next generation of cadets at the Academy.
Kaos and Glumshanks are sentenced to Cloudcracker prison since they still hold a record of crimes against the Skylands. Glumshanks tries to point out his master's hesitation to destroy the Core of Light but is quickly dismissed as Kaos is more focused on planning his future revenge against Kaossandra and his true father, Master Eon, angered for having lied to him all these years. Though Kaos still has to endure his prison time with the rest of Glumshanks' clones.
The Skylanders enjoy their relative peace time by playing sheep ball, but Spyro is in no mood to join them, still deeply upset and guilty for the events that have transpired that led to Eon's passing. The Skylanders try to cheer him up, believing that Eon is still with them if they continue to carry out his teachings. Spyro is thankful for their encouragement but decides to return to his room, still feeling dejected for their loss. But he is suddenly visited by Master Eon's spiritual form, and Spyro reacts in great bewilderment. Eon explains that the blast from the light spell did not kill him but actually sent him to another plane of existence. This has allowed Eon to travel known realms expansively and reveals to Spyro he has finally discovered where his dragon ancestors have been living, and offers Spyro a chance to finally meet them but the journey is a long one, and it would mean leaving the Academy behind temporarily. With some hesitation, Spyro accepts.
Spyro begins his long journey, accompanied by Master Eon. But Spyro glances back at the Academy, saddened that he would not see any of his friends for a long time. Spyro reassures Eon that he desires to meet his family, but first leaves a message for the entire Academy to see, before the two finally resume their travel.
While the Skylanders continue playing sheep ball, Stealth Elf is the first to notice, with the rest following suit, Spyro's farewell message: SKYLANDERS FOREVER! written from the clouds.
- Stealth Elf
- Pop Fizz
- Crash Bandicoot
- Coco Bandicoot
- Master Eon
- Trigger Happy
- Roller Brawl
- Bad Breath
- Food Fight
- Arkeyan Conquertron
- Crash Bandicoot and his sister Coco join the fight to protect the Core of Light.
- Strykore is imprisoned once again in the Endless Void.
- Master Eon reveals he is Kaos' real father.
- Master Eon sacrifices his physical form to destroy the Arkeyan Conquertron and save the Core of Light.
- Kaossandra takes over as headmistress of Skylanders Academy.
- Kaos, Glumshanks, and the army of Glumshanks clones are incarcerated at Cloudcracker Prison.
- Spyro temporarily leaves Skylanders Academy with Master Eon to see his dragon family.
- Upon seeing the Arkeyan Conquertron, Flynn gets a sense of déjà vu; a reference to the ending of Skylanders: Giants.
- Pop mentions that they've been fighting evil for three years, likely referring to the shows three seasons.
- When Master Eon returns in his spirit form, his beard has mysteriously returned to its original length from Skylanders Unite!.