Sensei Wu, Zane, and his Falcon are standing on a peak observing how the Dark Island has appeared in the middle of the ocean and how the Stone Army mysteriously disappeared. Zane sends his falcon to see what's on the Island while the others are working on the rocket boasters of the Bounty. Misako leads the others inside saying there is a way to defeat the Stone Army with in the scrolls. She tells them the power of the Green Ninja can only be unlocked when the four protectors (Kai, Jay, Cole, and Zane) find their true elemental power. She explains that they can find their elemental powers at The Temple of Light, which is located on The Dark Island. Since the Bounty can't fly, they decide to sail there instead.
The Bounty is placed at the dock, while everyone is saying their goodbyes to everyone they love, except for Zane. Zane tells Sensei Wu he will miss Ninjago but is excited for the future. The rest of the Ninja board the ship and set sail to the Island.
The Ninja ponder what they think is on the Island, but Lloyd wonders if it will be the end of their destiny. Zane checks his falcon vision and sees that he has arrived at the Dark Island, when a Stone Warrior shoots him down, leaving Zane with no family left. Misako than points out a storm heading their way.
Meanwhile on the Dark Island, Garmadon thinks its foolish "playing in mud" when the Overlord explains it's not mud, but Dark Matter, a horrible substance that can turn the kindest of man dark as night.
The Bounty crew struggle to fight the storm and are soon attacked by Starteeth, fish that devour ships until they sink. They use their Spinjitzu to throw them off board, but soon realize they have already chewed a hole in the ship.
On the bottom deck, the crew is trying to get all the water off the ship, when Zane claims he senses something. They crash on an Island which holds a large brick prison. They climb the stairs and are greeted by Dr. Julien, Zane's creator. He invites everyone inside and explains to Zane how he is alive, despite his memories saying he had passed.
After he turned off Zane's memory switch, Samukai revives him with an antidote and forces him to build vehicles and weapons for the army. When Dr. Julien refuses, the skeletons take him to the prison with a tool box and say once he has built everything, he will be able to see Zane again. Then, Samukai chained a Leviathan to the bottom of the sea, though Samukai never returned.
Suddenly, the Leviathan checks in on Dr. Julien while the Ninja and others hide. Kai and Nya ask Dr. Julien to fix the rocket boosters before "it" comes back.
They began to work together to fix the boosters. When Zane is finished cooking for his father, Zane asks his father to remove his memory switch so he will never forget his father. Dr. Julien explains that he is perfect just the way he is and is glad he found him. To ruin the moment, the Leviathan returns and they all run aboard the ship and try to fly away. When they are nearly pulled into the water, Zane notices the monster's chained, jumps into the ocean, and places Starteeth on the chain.
The monster is freed and releases the Bounty. Zane climbs back onto the Bounty and explains that "no one deserves be held captive. Not even a monster."