Amidst Ninjago's era of peace, Master Wu often spent time meditating to Spirit Smoke in his quarters, though on one occasion he was interrupted by the sound of the Ninja fighting. Curious he entered the training ground to find it deserted. He followed the cries of battle to the living room only to find the Ninja playing video games. Angered at the sight, Wu unplugged the TV and expressed his dismay about them neglecting their training. As a response to their angered outbursts, he began to speak about the power of the Golden Weapons and how they had let to unlock their True Potentials. The Ninja however ignored his warnings and returning to their video game, assuring their Master that they would be ready when Lord Garmadon returned. However at the moment, Nya arrived and informed them that Garmadon had in fact returned and was spotted approaching Jamanakai Village. Wu observed them rush to their dragons, displaying that they were clearly not in peak shape. As they flew away, Nya approached him and ask if they would ever reach their true potential to which he replied that they would "in time."
Later in the day, Wu was disturbed from his meditation to find the Ninja in the training course surrounded by flames. After using the Shurikens of Ice to extinguish the fire, Wu angrily demanded an explanation. The Ninja revealed they had discovered the prophecy of the Green Ninja and had been holding a tournament to determine who it would be, though Wu informed them that none of them had achieved the skills for the title.
Wu returned to the Spirit Smoke and saw a vision of the Hypnobrai attacking Jamanakai Village. He quickly sent the ninja on ahead and by the time he arrived at the village, the Serpentine had retreated. Now realizing that a new threat was upon them, the Ninja apologized for their lazy attitudes and implored their master to teach them the secrets of the Golden Weapons. Wu agreed and they returned to the Monastery.
Once again, Master Wu's meditation was interrupted by his pupils' noise-making, but he was pleasantly surprised to find them in the training course rather than the game room. He dissuaded the Ninja from questioning Zane's odd behavior and tried to comfort Zane when he became melancholy over not knowing his origins. Later, Master Wu ate dinner with his pupils and was dragged into a friendly food fight.
The next day, the Ninja set out to Wildwood Forest on a tip from Zane, who had stumbled upon Lloyd's Treehouse Fortress after following a mysterious Falcon. Master Wu initially remained at the Monastery of Spinjitzu with Nya, but only so he could prepare himself for the battle against the Serpentine. He and Nya flew to the forest astride Flame's back, only to find the fortress crumbling and Cole attacking his allies (due to Skales' hypnotism). Recognizing the signs of Hypnobrai Hypnotism, Master Wu played the Sacred Flute, breaking the spell and allowing the Ninja to escape the fortress moments before it collapsed completely.
On their way back to the monastery, Master Wu explained the flute's significance to the Ninja, claiming that it would play a large part in the defeat of the Hypnobrai. When Flame returned to the monastery, the group was horrified to see it completely destroyed—the Hypnobrai had burned it to the ground after retrieving their staff. As the Ninja rushed to free the other dragons from their burning stable, they blamed Zane for their loss, prompting Master Wu to rebuke them for their rash anger. Before the Ninja could apologize, Zane had already flown into the night on the back of his dragon.
Despite the loss of their home, Master Wu remained optimistic as he and his pupils erected a meager shelter from what they could salvage from the Monastery. The next day, Zane returned and explained that the Falcon had led him to a new home: the Destiny's Bounty. As the Ninja rushed to explore the ship, Master Wu promised that they would help Zane find his family, only for Zane to reply that they were his family.
As the Ninja worked on restoring the Destiny's Bounty, Jay's parents, Ed and Edna, came by to visit their son. Master Wu watched in amusement as Jay struggled to remain calm despite his parents' embarrassing antics; commenting afterwards that the Blue Ninja could teach them all "the art of kissing pillows." The next day, he noticed that the Ninjas' dragons were molting, and told his pupils that the beasts would have to go to the Spirit Coves to complete their metamorphosis.
After seeing the dragons off, Master Wu joined the others in walking to Ed & Edna's Scrap N Junk so Jay could visit his parents. Upon arrival, they found the owners stuffed in a fridge, slowly transforming into snakes. Master Wu immediately realized that Ed and Edna had been bitten by the Fangpyre tribe, a suspicion confirmed when the Fangpyre revealed themselves, along with Lloyd (who had released them in hopes of getting revenge on the Hypnobrai who betrayed him).
The Ninja immediately jumped into battle, fending off the snakes and their new vehicles while Master Wu began playing the Sacred Flute to weaken the Serpentine. Unfortunately for him, Lloyd drowned out the music with a Fangpyre-infected boombox; when Master Wu demanded that Lloyd stop that, his evil nephew simply turned up the volume and claimed not to hear his words. In the confusion, Master Wu was almost bitten by a Fangpyre Scout, but Edna knocked him out with a frying pan.
The Fangpyre were eventually forced to retreat, but their staff and its anti-venom was still in the hands of General Fangtom. To save Ed and Edna, Master Wu told the Ninja about the Golden Weapons' ability to transform, and the Ninja soon manifested vehicles of their own with which to pursue the fleeing Serpentine. Jay managed to retrieve the staff, but his inexperience with his new vehicle caused him to lose focus, reverting the jet to its original form. The other Ninja soon followed, and the group barely escaped back to the Destiny's Bounty with the anti-venom.
One day, Master Wu discovered the Ninja slacking off their duties in order to discuss a dream Zane had about the Green Ninja. As punishment, he made them train constantly until they could answer a riddle: "What is the best way to defeat an enemy?" Over the course of the next few days, the Ninja alternated between training and pondering the riddle, but nothing they thought of proved to be correct.
However, more pressing matters arose when Lloyd resurfaced with a new ally: Pythor P. Chumsworth, Serpentine General of the dreaded Anacondrai tribe. The villains took over Darkley's Boarding School for Bad Boys, forcing the Ninja to head out—Master Wu and Nya followed in the Destiny's Bounty, arriving just in time to see Pythor betray Lloyd by stealing the Map of Dens and leaving him to be apprehended. Despite the Ninjas' demands that Lloyd be punished terribly, Master Wu insisted that he take care of his nephew, and proceeded to give him a home aboard the ship. When the Ninja protested, Wu revealed the answer to his unsolved riddle: "The best way to defeat an enemy...is to make him your friend."
The Ninja realize they may have reached their full potential, and accidentally disturb Wu while he is packing. He tells them the story of how and why Garmadon was bitten by the Great Devourer and turned evil, before telling them they have completed their training. He then leaves for Mistaké's tea shop for Traveller's Tea, and uses it to travel into the alternate dimension Lord Garmadon had escaped into in search of his help in getting Lloyd back and defeating the Serpentine.
Garmadon confronts Wu and a battle ensues, with Garmadon summoning the Mud Monsters to consume Wu. Wu tells Garmadon that Lloyd is in danger, and Garmadon rescues Master just in time to prevent him from dying. They then journey to the Mountain of Madness.
After returning to Ninjago, Wu brought Garmadon to the Bounty, much to the dismay of Kai.
After the team decided to travel to the Serpentine's fortress, Wu was informed that Nya and Jay made a modification to her Mech so that he could come along.
However, after a short fight, they were trapped in a Vengestone cage and had to wait for Lloyd to rescue them.
Wu is meditating with the aid of his Spirit Smoke. The smoke shows him a vision of Pythor awakening the Great Devourer, causing Master Wu to come to a horrible realization. Later, as the Destiny's Bounty arrives over Torchfire Mountain, Wu tells the Ninja that he "will not be able to see tommorow" whilst the ninja proceed to set up a plank from where they can throw the Fangblades into the volcano. Unfortunately, Pythor chooses that moment to sabotage the engines, jerking the ship to one side and throwing Master Wu over the edge. The Ninja form a human chain to catch their teacher. After Pythor got the four fangblades, he alerts his minions to prepare for a fight and the Fangpyres use their venom to transform the bus into the Serpentine Train. Later, Master Wu leaps onto the front car and separates it from the rest of the train, declaring that battling Pythor is his destiny, while his students' destiny is to protect Lloyd. Master Wu fights Pythor, but does not succeed to stop Pythor from releasing the Great Devourer. As Pythor tries to leave in fear, Wu holds him back, saying that he "must witness what he has created" and tells the ninja that it's his destiny and that they must do anything they can to stop the Great Devourer.
Master Wu is consumed by the Devourer, and is only seen at the end of the episode after Garmadon destroys the Great Devourer. He finds his tea kettle among what is left of the Devourer, commenting that it is still hot.