Returning to Arcadia, Douxie tries to protect Nari from the Arcane Order and retrieves Krel Tarron from the wreckage of a fight at Hex Tech. The other heroes face Bellroc and Skrael in an epic battle aboard the Arcane Order's ship; Morgana and Arthur battle each other on the ground, while Claire, Toby, Blinky, and AAARRRGGHH desperately try to save Jim's soul. At the end of Jim's fight with his friends, he turns into stone and dies. As Claire hugs Jim's stone form and cries, a tear falls off her cheek, landing on stone Jim and causing him to explode. From the rubble rises Jim in his original human form, but he no longer has the Amulet of Merlin or the powers of the Trollhunter.
Morgana causes a large section of Camelot to fall and crush Arthur, unfortunately killing herself, too. Douxie, meanwhile, is gravely injured in his battle with the Arcane Order. The spirits of Douxie, Morgana and Merlin have a final conversation in Merlin's old library before Morgana and Merlin walk through a door into a bright light (presumably the gate to Heaven) and Douxie's soul returns to his body. Douxie vows to spend the rest of his life protecting Nari from the Arcane Order to prevent the breaking of the Genesis seals.
When Arthur dies, Excalibur is stuck in a stone. Jim and Toby try to remove the sword, but to no avail. Douxie assures them that the greatest strength they have is the one they get from their friends. Douxie, Archie and Nari leave on Merlin's airship while Jim, Claire, Toby, Steve, Blinky, AAARRRGGHH and Krel remain behind as the champions tasked with protecting Arcadia from future threats. The series ends a short while later, with Nari and Douxie walking on a street in New York City while Bellroc watches them from atop a building, planning her revenge.