Plot:
The goal of the game is to capture the villains who have escaped from Cloudcracker Prison. Long ago, Skylands was ruled by powerful villains called the Doom Raiders who hid out in the Savage Badlands and wreaked havoc over Skylands. They were eventually captured by the Trap Masters and remanded to Cloudcracker Prison.
A few years later, Kaos, the game's main antagonist, released The Doom Raiders and the other villains by blowing up Cloudcracker Prison. As a result, the Trap Masters were also sent to earth along with crystal traps formed by a material of the prison called Traptanium. During the opening of Skylanders Academy presented by Buzz, a remnant of the explosion is seen and he goes to investigate. Buzz helps the player's Skylanders catch the Gulper, a gluttonous blob monster, at Soda Springs by using his addiction to soda.
Meanwhile, Kaos gathers with the Doom Raiders at his new base, but the Doom Raiders reject Kaos without even listening to his plan due to him failing to stop the Skylanders from recapturing the Gulper. The Raiders' leader Golden Queen, an animated statue capable of turning objects to gold with a single touch, lets Kaos and Glumshanks stay, only to come up with a plan of her own.
After capturing The Gulper, Buzz and the Skylanders are informed of Cloudcracker Prison's destruction by the creator of the Academy, Mags, and sets to capture the remaining villains. The Skylanders secure intelligence about the Doom Raiders at Know-It-all Island, then head to Chompy Mountain, where they battle the Chompy Mage (a mage obsessed with Chompies who they met in Skylanders: Giants) and his forces, and trap him. Meanwhile, the Doom Raiders learn of the defeat and dissent grows in the ranks, with Kaos deciding to take advantage of this to retake control.
The Skylanders are sent to track down Fire-elemental Doomraider, Chef Pepper Jack, who is an anthropomorphic chili pepper who was formerly a celebrity chef. Meeting up with Tessa at Phoenix Psanctuary, they hold off the Chef's forces from obtaining a Phoenix Chicken egg to create a Spicy Omelet of Doom. Kaos intervenes to sabotage the plans, but his smoke rocket lets Chef Pepper Jack escape with an egg. Launching an assault on his Zeppelin, the Skylanders free all the slaves on board, and trap the maniacal cook. With 3 Doom Raiders down, the remaining Doom Raiders are set to take action, but the Golden Queen still wants to build a weapon made of Traptanium in an attempt to steal all the riches of Skylands, much to Kaos' dismay. He tries to reassert control, but loses.
After acquiring an Information Squid from Mags's home village, the Skylanders try to figure out why the Doom Raiders are obtaining Traptanium. Eventually, Mags's Information Squid turns out to be Kaos in disguise who soon forms an unlikely alliance with the heroes. With Kaos being the only lead to where the Doom Raiders are, the Skylanders travel to Monster Marsh where they find Dreamcatcher, who's a sadistic and immature floating head that's able to manipulate dreams and bring nightmares to life, has been terrorizing a Mabu village. They are able to stop her by waking the sleeping townspeople, but she escapes. The Skylanders head to Telescopic Towers to prevent her from stealing secrets of Traptanium from the dreams of Mabu scientists, eventually defeating and trapping her, though she manages to send the secrets to the Golden Queen regardless.
Though the secrets were lost, Dr. Krankcase, a mad scientist specializing in animating wood into evil robotic minions made of wood, still needs one final piece to the weapon: a large amount of "stinkocity", or bad odor. While the Skylanders manage to stop the main flow of smelly goo, Dr. Krankcase substitutes the goo for cheese, and comes up with a plan to simply bury it and travel forward in time to when it will be unbearable in stench, though this requires a Portal Master. To do so, they reopen Kaos' old workshop and trap him, but Wolfgang, a rockstar werewolf armed with a massive bone harp, abandons Dr. Krankcase and leaves him to be trapped by the Skylanders.
The Skylanders and Flynn track Wolfgang to Time Town, but they arrive too late as Wolfgang has already headed to the far future. Arriving in that time period, they discover that Wolfgang has completely taken over and constructed the "Big Bad Woofer", a giant speaker that amplifies his painful music 10-fold. The Skylanders make their way to the sinister speaker and shut it down, and defeat Wolfgang. However, the rotten cheese was sent to the Golden Queen in the present, and she completes the weapon. Holding Skylands hostage, she demands her fellow Doom Raiders to be freed and all the gold in the world as tribute.
The Skylanders and their comrades steal a rocket from the Trolls and use it to get to the Skyhighlands, where they find a crystal to locate the Golden Queen's lair. Traveling there, Cali is imprisoned in gold, and the Skylanders have to fight their way through the lair to rescue her. In an epic battle against the Queen, the Skylanders are victorious in trapping the queen and putting and end to her tyranny once and for all. However, Kaos takes the weapon for himself and absorbs the combined stinkocity and energy from the collected Traptanium, to become much stronger. He then realizes it was not the Skylanders he had to destroy, but the one thing that was always in his way: the Portal Master, or the player, and sets his sights on Earth. With both worlds hanging in the balance, the Skylanders make their way through the weapon and battle Kaos, who transforms into an enhanced Traptainium version of himself, growing Traptanium swords and raven-like wings. In spite of this, Kaos is finally defeated and put in a trap of his own. The weapon then overloads and explodes, freeing the trapped cities. The game ends with the residents of the academy celebrating.
Features:
The player is able to use traps of different elements to capture villains after defeating them. When the player places the trap into the portal, they get to play as that villain who is now on the good side. The game alos comes with a new portal of power that comes with a built-in audio speaker that allows players to hear the voices of the villains travel from the game into the real world Trap, and vice versa. The Trap also lights up in sync with the villain speaking.