As the game opens, Kaos narrates his previously failed plans as he tells the Portal Master that he has captured Master Eon, Flynn, Cali, and Hugo. Now that Kaos has control of the portals, he tells the players that they are getting cut off from Skylands forever. Hugo manages to get through to the Portal Master stating that they must place a land vehicle on the portal so that they can get the Skylanders to Skylands. Once that is done, the Skylanders infiltrate a transport ship owned by Count Moneybone where they manage to free Hugo, Cali, and Flynn. Hugo tells them that there are other prisoners on the transport ship that need to be free too. Upon getting topside, Flynn, Cali, and Hugo see a contraption that is "eating the sky." Hugo's book glows as Master Eon's message states that he has been taken captive and that Kaos has used the Darkness to construct the Sky Eater. In order to combat it, a special team of Skylanders called the SuperChargers have been assembled to help combat the Sky Eater utilizing special rift engines that utilize the same technology as the portals.