It had been 3 months since Spyro and Cynder first came to Skylands, and they already had many adventures. One of them was to save the Radiant Isles from a being called Hektore, another was to help Cloud Patrol recapture trolls that escaped prison, and another was to help Advisor Orville establish a home for Mabu in the Lost Islands. There was also a Dark Portal Master who was called Kaos who wanted to take over Skylands. For being an assistant to the Darkness, Kaos was banished to the Outlands. Spyro was intimidated when he saw his giant floating head for the first time, but in person, he just couldn't stop laughing at how much of a pipsqueak Kaos was. He also went with Gill Grunt, Eruptor, and Boomer to stop Kaos from acquiring The Machine of Doom, a giant war machine that was part of the ancient race known as the Arkeyans. The only two Skylanders who WERE Arkeyans were the Undead Knight Chop Chop, and the Tech Robot Drill Sergeant. Spyro had also faced Mega-Monsters, Grill Grunt had undone a curse unleashed by an evil fish master called Grimslobber, Lightning Rod faced an evil Cyclops Queen, Terrafin battled a deadly duo known as the Boom Brothers, Cynder stopped an evil weather wizard known as Hurrikazam, Stump Smash took on a deadly bone dragon, Eruptor learned about an evil king known as Nefarion, and Trigger Happy stopped Kaos from piecing together the Mask of Power! According to Eon, when Spyro and Cynder came to Skylands, they had half of their memories wiped, thus making them only remember certain events in their past. The Skylanders were also tasked with protecting the only thing that could repel The Darkness: The Core of Light. Built by the Benevolent Ancients, it was a machine powered by all eight elements via the Eternal Elemental Sources. Kaos planned to destroy it, but all his attempts had failed. However, something told Spyro that this next one would be very, very different. Then, he, Trig, and Eon noticed dark clouds. Spyro knew that it meant one thing: The Darkness had returned. "M-m-m-master Eon!" Hugo stammered, running in. "T-t-t-those clouds! Is something wrong?!" "Have you ever known dark boiling ominous clouds to be a good thing, Hugo?" Eon asked. Hugo shook his head. Then, a black flying castle emerged from the clouds! This could only mean one thing. Kaos had returned! "Take your station, Hugo!" Eon instructed. Hugo then ran for cover. "Skylanders!" Eon cried. "The Darkness has come! Prepare for battle!" Then, something huge emerged from the clouds! "BEHOLD!" The giant head boomed. "It is I, Kaos! Long have I waited for this day to take my revenge! Soon, you will all bow down before me! Kaos! K-A-O-S!" "Kaos! I might have known!" Eon said. "And what happened to your head? It looks ridiculous!" "AH!? What?! My head is AWESOME, I tell you! Fear it! Fear my giant floating head!" Kaos roared. After a brief silence, Kaos continued his evilness. "You thought you had banished me to the Outlands, didn't you?! HAHAHAHAHA! I, Kaos, have returned to destroy the Core of Light and rule Skylands as its emperor! And you are now so old and weak, Eon! There is nothing you can do about it! AHAHAHAHAHA!" "I've told you before, Kaos!" Eon said. "You and the Darkness have no power here!" "Oh, is that so?" Kaos yelled. "We'll just see about that! MINIONS!" Then, evil minions were beamed down to destroy the Core of Light! "Skylanders! To battle!" And with that, the battle began! "Game On!" Spyro yelled as he beamed down onto the field. He then charged into Cyclops grunts and head-butted them, while Gill Grunt used his harpoon to take on a Goliath Drow. Terrafin took on a Troll Brawler and eventually went in for the K.O. He then burrowed after more Cyclops minions and belly-flopped them. Stump Smash chased after more minions, his fists pounding. Hugo watched this from his rock cover. Trig was as backup as he shot Cyclops Mammoths. He then charged up to shoot more Drows while Stump Smash spat out acorns. Spyro then breathed fire at more minions while Terrafin made a Cyclops take a belly-flop to the face. Slam-Bam slammed two minions together, then tossed the other two to Stump-Smash, who took them out with a spin attack. Trigger Happy and Wrecking Ball made coins and tongues flying as Goliath Drows were getting pummeled. Zap and Eruptor burned and shocked more enemies that surrounded Wham-Shell and Stealth Elf. Spyro dodged a catapult strike as he flew into more minions. Boomer made trolls get blown up. "Uh-Uh! I don't think so!" Cynder said as she carried of a troll warrior who had disarmed Gill Grunt and was about to have sushi. However, just as all seemed won, something huge came out of the castle! "Not the CORE!" Then, the Core of Light was blown up by a very, very, VERY big BOOM (which was also Flynn's catchphrase)! Before Spyro could do anything, he and the others found themselves whisked away, and the dragon watched helplessly as Eon was pulled into his own portal. Spyro tried to scream "NO!", but he couldn't. In fact, he couldn't move at all! Then, he felt Skylands get more and more distant as he and the others were speeding away from it. Spyro then felt very small. Maybe this is how he would die. And then, with a sudden boom, it all ended.
Spyro didn't know where he was, or how he got there. Well, he knew the second part. There was this giant pink creature that carried him towards a building. Then, the creature noticed a portal, but not before Spyro noticed himself in a wall of glass. He looked like… a toy? This made no sense at all! Then, he was placed upon the portal. He heard it humming. Then, he felt life flowing through him! Finally, he broke free of his small prison and came back to his normal size. Spyro shook off pieces of rock and looked at himself, moving his wings and talons and looking at them. A smile crept along his face. Then, the creature grabbed a weapon in fear. "Stay back!" It yelled. "Don't come any closer!" Spyro stayed on the portal. He swished his tail, bowed, and purred. The creature lowered the weapon, then touched his snout. Smoke flared out Spyro's nostrils. Then, something materialized beside him! It was… Eon! But how?! Spyro thought he was dead! He was pulled into his own portal! "Greetings, young Portal Master!" Eon's spirit said. "AAAAHHH!" The creature yelled, stumbling back and hitting his head on a bookcase. "Do not be alarmed." Spirit Eon said. "Spyro and I mean you no harm. I have been waiting for you. I am Eon, the greatest Portal Master that ever lived." "Spyro?" The young Portal Master apprentice asked. "Is that your name?" Spyro nodded. The Apprentice turned to Eon. "Waiting for me? What do you mean?" "Allow me to explain." Eon moved aside, revealing an image of Skylands. "Spyro and I come from a world beyond your own. This is Skylands. It lies at the very heart of the universe. It is full of magic, wonder, and adventure." "It's…. amazing." "That's exactly what Spyro told me when he arrived." "Wait." The Apprentice turned to Spyro. "You can talk?!" Spyro tried to say yes, but the lack of Skylands' magic made his vocal cords useless. He just shrugged and shook his head in response. "I will get to that later." Eon said. More images appeared, acting like a living storybook. Eon then explained to the Apprentice about the Portal Masters, the Darkness, The Core of Light, the Dark Portal Masters, Nefarion, the Skylanders, Kaos, and how the Skylanders came to this world, which was called Earth, as it was a planet. It was apparently the homeworld of all the Portal Masters-to-be. Then, Eon faded away as the portal built up magical energy. Spyro extended his wings and braced himself. "Thank you, Portal Master." He said to the Apprentice. Then, in a beam of purple light, he flew back to Skylands.
Spyro made a perfect landing in Shattered Island right in front of Hugo! "WOAH!" Hugo cried. "Spyro! You've returned!" Then, the dragon noticed two other meteors. One dark blue, and one gold. The dark blue one went off target and crashed on a lower island, while the gold one crashed right into the nearby windmill! Gill Grunt clutched his head and found himself alive, while Trigger Happy cried out "I'm okay!", in a crazy tone. "Master Eon was right!" Hugo said ecstatic. "That means he DID find another Portal Master to help us! Come on Skylanders! This village needs our help!" "Well, you can count me in! I'm all fired up!" Spyro then flew over the bridge, but before Hugo could cross, a flying rock smashed it! "HUGO! Are you alright?!" "Don't worry! There's a balloon just nearby!" As the trio rushed through the village, they were able to reunite with Flynn. "See that twister?" Flynn yelled over the wind. "Yeah. It's coming from the Darkness!" Spyro said. "I've got an idea!" Flynn said. "What we're gonna do is-WOAH!" Flynn ran to his balloon and flew off. Gill ran, but the flying rock knocked him off! Trig jumped and Spyro caught himself. Then, they found themselves face-to-face with Chompies! Spyro smiled. This was too easy. After dealing with the chompies, the trio managed to get to the castle and save the Mabu Royal Family. When the hero work was done, the trio went with Flynn and Hugo on Flynn's balloon back to the Citadel to reunite with the other Skylanders.