The Episode begins a few centuries before the present, with the pirate crew of the Destiny's Bounty captained by Captain Soto looking for the Dark Island. The crew leave No Eyed Pete to steer the ship when the captain wasn't noticing, but due to his lack of sight, they crash in Ninjago.
In the present time, Kai is training Lloyd Garmadon in their apartment, referencing the moment Sensei Wu told Kai "You are not ready to face my pinkie toe". Later Lloyd goes to visit Nya and the Ultra Dragon at the top of a building in Ninjago City. Nya tells Lloyd that the Ultra Dragon now belongs to him since the Ultra Dragon is meant for the green ninja (the ultimate spinjitzu master).
Later Sensei gives the ninjas bus tokens to go and find a better place to train.
On the Black Bounty, Lord Garmadon is discussing the one weapon with the Snake Generals, and he tries to use it to destroy the Ultra Dragon, who was fling close to the Bounty. He flies into a rage when he is unable to destroy it, and discovers Captain Soto's journal in the cabin. He accidentally resurrects the pirate crew, then finding out that the weapon can only create and that it weakens him when used. Captain Soto then orders his crew to lock up Garmadon, who is unable to defeat them because he is weak, and the Serpentine in the brig.
Meanwhile, the ninja find "Grand Sensei Dareths Mojo Dojo" where there introduced to "Grand Sensei" Dareth. Dareth agrees to let them use his dojo if they defeat him in a battle. Kai then defeats Dareth with Spinjitzu and he allows them to use his dojo. The ninjas start training Lloyd at a dojo, where he demonstrates powers of the Scythe of Quakes. When Lloyd is told to break boards, he accidentally cracks the floor in the process. Zane comments that the reason he has the potential to be the greatest Ninja is because he can master all of the elemental powers. Dareth, though, is not impressed. He tells the Ninja he could chop fifty boards in half and says if he does so, the Ninja would have to make him the Brown Ninja, although he fails miserably.
Soon after, the Pirates begin flying the ship through Ninjago City. The Ninja are instantly alerted and head after it, telling Lloyd he needs to stay behind since his powers are too uncontrollable. However, Dareth gets on board first, convinced that if he stops the pirates he’ll be allowed to be the Brown Ninja. He is soon captured, and the Ninja decide to sneak on dressed up as pirates.
The Pirates then attack Ninjago city. On board, Dareth is forced to walk the plank. He confesses that all his trophies are fake and his brown belt is coloured before falling off, only to be caught by the Ultra Dragon, who is being driven by Lloyd. The Ninja shed their disguises and fight against the pirates using their wooden weapons. When Lloyd drops in, they tell him not to fight and Kai puts him in a barrel to keep him from fighting. In an attempt to get out of the barrel, Lloyd uses his first Spinjitzu, and Garmadon and the Serpentine are freed from the jail cell in time to see Lloyd has become stronger. The pirates are later arrested, and Lord Garmadon takes back the Black Bounty.
When Jay says "Look pal, we're the guys that just saved the city from a giant snake", he says it with Cole's voice.