With the Devourer defeated, the Ninja found themselves with a new problem: the loss of the Bounty during their battle with the Devourer meant that they no longer had a place to live. While Nya and Wu left town to find parts for the Ultra Sonic Raider, Lloyd and the others sought out new living arrangement, and after visiting a tiny dwelling were shown a massive apartment that seemed perfect for their needs. Unfortunately, the older Ninja became so busy working so that they could afford their new home that they were unable to train Lloyd. Worse yet, Lloyd was targeted by the Serpetine Generals for abduction in an effort to regain leadership of the tribes after they sided with Lloyd's father. Fortunately, Nya and Wu arrived in time to save him, and the other Ninja soon chose to relocate to the smaller apartment they had been shown earlier.
The next morning, Lloyd trained with the Ninja in their apartment, though they soon realized their situation was unsuitable to properly prepare him for the final battle. After Lloyd learned from Nya that the Ultra Dragon would belong to him, the Ninja began searching Ninjago City and soon came across Grand Sensei Dareth's Mojo Dojo where they made an agreement with Dareth to train there.
Their first session there proved successful as Lloyd was even able to use the power of the Scythe of Quakes without the Golden Weapon. As the Ninja exited the dojo, they were surprised to find the Destiny's Bounty passing by, rebuilt and commandeered by pirates. The Ninja boarded a city bus to pursue, though they refused to let Lloyd come along. Undeterred, Lloyd summoned the Ultra Dragon and used it to rescue Dareth as he fell off the flying vessel. The Green Ninja then jumped onto the ship and joined the Ninja during their fight against the pirates. Amidst the battle, Lloyd was able to unlock Spinjitzu for the first time, though with his powers still uncontrollable, he accidentally destroyed the ship's mast.
The Ninja later received an unexpected letter from Lloyd's old school, claiming that they wished to honor Lloyd with a degree in response to his decision to become good. However, it turned out to be a trap orchestrated by Lloyd's former classmates, who had taken over the school after it had changed to good. Lloyd's classmates attempted to turn him back to the dark side, particularly after the Bizarro Ninja arrived looking to destroy their heroic counterparts. However, Lloyd helped them all to realize that each of them was secretly good, and they joined forces to help the true Ninja defeat their evil clones.
While attempting to balance on one hand while also balancing his allies on top of himself, Lloyd's training was interrupted by a wrecking ball smashing through the wall of the dojo. Learning that Dareth's dojo was scheduled to be condemned due to unpaid bills, his allies realized that Lord Garmadon was behind the plan, in hopes of leaving the Ninja with nowhere to train. To save the dojo, the Ninja decided to enter the annual Ninjaball Run, which offered a substantial amount of money for the victor.
Lloyd entered the race astride the Ultra Dragon, while his fellow Ninja entered in the Ultra Sonic Raider. Although they were left in the dust early on (due to sabotage by Brad and Gene), they quickly began to close in on the competition as they entered Crashcourse Canyon. Lloyd was so busy trying to catch up, he didn't realize that Lord Garmadon had entered the race until the Ultra Dragon bumped into the Black Bounty, ruining its shot on the Raider. Following this incident, Lloyd and the other Ninja decided to work together to get in the lead.
As the competitors entered Birchwood Forest, Lloyd flew the Ultra Dragon high into the sky to look ahead. He spotted a shortcut for the Ultra Sonic Raider, only to be yanked out of the air by the bone hand of the Skull Truck (although this also caused Kruncha and Nuckal to crash). The Ninja were forced to carry on without Lloyd while he tended to the rattled Ultra Dragon.
After the Ultra Dragon recovered, Lloyd flew back to Ninjago City, where the Ninja had narrowly defeated Lord Garmadon to win the race. Noticing that the Black Bounty was unoccupied, Lloyd landed the Ultra Dragon on the ship and claimed it for the Ninja once more. Unfortunately, Garmadon escaped when Skales turned up in the Serpentine Bus, but Lloyd was still able to share a hearty laugh with his friends as Dareth gleefully celebrated their victory by diving into the large, money-filled trophy.
Soon after, Lloyd watched some children play ball in Jamanakai Village as the Bounty flew past, but was ordered by the Ninja to train soon after. Shortly into their training however, Nya reported that Garmadon had been spotted at the history museum, though Lloyd was forbidden to accompany them as usual.
The next day the Ninja still had not returned and though Lloyd was supposed to be reading a training manual, he instead read an issue of Starfarer when Sensei and Nya left to search for their missing comrades.
Still awaiting word from the Ninja, Lloyd turned to playing video games around the time he received a phone call from Jay ordering the Green Ninja to Buddy's Pizza and to bring their weapons. Lloyd obeyed and was stunned to discover upon arriving that the other four had been turned into kids by Garmadon's Mega Weapons. Worse, the weapon had also awoken a Grundle which was now after the Ninja.
Seeking help to defeat their foe, Lloyd brought the other Ninja to Doomsday Comix where he asked Rufus MacAllister for advice. Determining that Illumiswords would be needed in stopping it, Lloyd entered in the Fritz Donnegan trivia battle-royale to win them. The Green Ninja made it to the final round, but as he had not read the latest issue of Starfarer, he lost to another fan.
It was then that the Grundle attacked and the Ninja bravely protected the other fans present. Wu and Nya soon arrived with Tomorrow Tea and gave it to Lloyd to use on the Grundle. The Ninja urged him not to use it as it would also turn the Green Ninja older as well, causing him to loose the rest of his childhood. Accepting it as his fate, Lloyd used the Tomorrow's Tea, thus destroying the creature but aging him significantly as well.
In his new teenage form, Lloyd discovered that he had become a far more efficient ninja, learning quickly and displaying a new motivation for training. He rapidly became skilled enough to battle all four of his peers simultaneously, although he still made the occasional basic error. After one such error—concentrating on blocking Kai's sword, allowing the Red Ninja to pull the blade away and cause him to fall—Lloyd expressed regret for not taking his training seriously before the Grundle incident, but Sensei Wu assured him that they could only change the future, not the past.
One day, the Falcon returned to the Destiny's Bounty with troubling footage—Lord Garmadon and the Serpentine were back in the Lost City of Ouroboros, apparently preparing for a final battle. Lloyd accompanied the Ninja, Nya, and Sensei Wu to the city that night, where they confronted Lord Garmadon. Lloyd jumped in as his father tried to use the Mega Weapon, firing an ice beam to freeze the tip of the staff. He took Garmadon's shock at his older appearance in stride, commenting that he'd "grown a little" since their last meeting. Before the heroes could attack, Lord Garmadon fled, leaving a group of Serpentine soldiers to attack them.
The Ninja quickly defeated the snakes and pursued Lord Garmadon, only to find an empty room and a strange portal before them. Suddenly, the City of Ouroboros began to sink into the sand, and Lloyd realized that he could not feel his hands. Everyone realized that Lord Garmadon had traveled into the past, attempting to negate Lloyd's destiny by preventing the Ninja from becoming a team. As the other four Ninja leaped into the portal to stop Garmadon's time tampering, Lloyd joined Nya and Sensei Wu in fleeing the city before they were buried alive.
Lloyd presumably returned to the Destiny's Bounty and waited for his friends. During his wait, his destiny was repeatedly altered by the actions of the Ninja and Lord Garmadon in the past, causing him to disappear and reappear aboard the ship. Eventually, however, the Ninja managed to restore the past to its original form by destroying Garmadon's Mega Weapon with the Golden Weapons of the past.
When the timestream repaired itself, the Ninja were taken back to the previous night, at the beginning of their training session with Lloyd. Lloyd himself arrived late, but barely had a chance to apologize before the other Ninja hugged him, visibly relieved. He was puzzled by their talk, wondering why he wouldn't be here with them, and his confusion only grew when they began speaking of Lord Garmadon's Mega Weapon—its destruction in the past had erased his memories of it. Eventually, however, the Ninja told Lloyd not to worry about the past and prepare for the future, although Lloyd still felt like he was missing some sort of joke.
On a Wednesday morning, Lloyd and the other Ninja were met by Sensei Wu who informed them that the Ultra Dragon made a mess outside. Though Lloyd played a game of rock, paper, clams against the other Ninja, he ended up having to clean up the mess outside. However before he could take care of it, Nya rushed in and told the Ninja of an emergency at the Ninjago Museum of History.
When the Ninja arrived, the museum's director revealed them that the Great Devourer's venom had seeped into the sewer system and leaked into the museum and brought the Stone Warrior merchandise to life. The Ninja then dealt with the little miniatures, though made a mess in the process. Once finished, they met up with Wu who had stumbled upon Lloyd's mother, Misako. Still enraged that she left him when he was young, Lloyd stormed off into another room to be alone.
Misako eventually found Lloyd sitting at the edge of a bottomless sinkhole exhibit, where she Misako explains that she abandoned him in order to learn everything about the Green Ninja prophecy, knowing that Lloyd would be the Green Ninja and wanting to stop him and his father from fighting the final battle. She then told him of the First Spinjitzu Master's battle with the Overlord.
Then, while the Museum Director showcases the new Stone Warrior Statue exhibit, some of the Great Devourer's venom drips from the ceiling and onto the exhibit, bringing it to life. As Misako tells them that there is no hope to prevent Lord Garmadon and Lloyd's fight, the Stone Warrior starts rampaging through the Museum and confronts the ninja. They try to fight it off, which was ineffectual, and they are forced to flee the room and run through the museum as they try devising a plan to defeat it. They stop inside a large room and close the doors, and as the Stone Warrior begins to break it down, Lloyd suddenly comes up with a plan and tells the Ninja to distract it. Lloyd leaves the room and the Stone Warrior breaks in.
At the museum, Misako decides to help Lloyd by leading the Stone Warrior to Lloyd's location. After she meets up with him, Lloyd manages to trick the Stone Warrior into stepping over the fake floor paneling, revealing the giant sinkhole where it was unearthed. Once the warrior falls, Misako tells Lloyd that she is proud of her son, and when Sensei Wu arrives he asks her to stay with them, to which she accepts.
Lloyd was training to fight without using his eyes (messing up Dareth's Dojo in the process) when Ninjago City was hit by a strong earthquake. The Ninja saved a woman who was trapped by the collapsing street as Misako realized that, according to the prophecies, the earthquakes are a warning. Soon after, an army of Stone Warriors emerged from underground (accidentally awoken by the Great Devourer's venom and released from their tomb by Skales' Serpentine) and wreak havoc over the city. At Sensei Wu's instruction, Lloyd and the other Ninja held off the warriors as best as they could while the citizens evacuated to the roof of the NTV office building.
The ninja sail to the dark island via flightless Destiny's Bounty. Along the way they run into a storm and ship-eating Starteeth. When the storm passes the ship (without a rudder and a hole in the side) runs ashore on an island with a prison tower. When the ninja get to the top, Dr. Julien greets them and takes them in. Inside he seats them and haves a robot serve them tea. There, Dr. Julien tells Zane what happened after his apparent death.
After Dr. Julien turned off Zane's memory switch, he really did pass away, but Samukai revived him with a special elixir, and in return, requested that he create the Skeleton Army's vehicles. When Dr. Julien refused, Samukai locked him in the prison tower with a Leviathan to keep guard, promising the doctor if he did what he said, he would see Zane again. However, time elapsed.
After he finished telling his story, the Leviathan comes and sends out a tentacle with eyes to check on Dr. Julien, while the others hide. After it goes away, Dr. Julien and the ninja work together to fix the Bounty's rocket boosters.
As the Bounty takes off, the Leviathan grabs the ship. Zane jumps into the water and frees the creature from its chains using star teeth. Freed, the Leviathan lets the Bounty go, and the Ninja all sail off back to Ninjago.
The ninja finally arrive on the Island of Darkness, where the Stone Army is preparing for the final battle. Lord Garmadon oversees the army's mining of Dark Matter, pure evil in the heart of the island, in order to build a superweapon that can turn the tide of the war.
On the Destiny's Bounty, the Ninja learn that the Temple of Light is where they can receive their elemental powers and where Lloyd can gain the Ultimate Spinjitzu Master technique: the Golden Dragon, a fighting style practiced only by the First Spinjitzu Master. In order to do this, the ninja must use a medallion to find the temple, where Lloyd must strike the Instrument of Peace. The Ninja prepare to head out, but Sensei Wu tells Lloyd to stay behind—they cannot risk starting the final battle early by having him encounter his father. The sensei also tells his pupils to remain stealthy at all costs, as Garmadon does not yet know they are here—unbeknownst to the heroes, the Overlord has sensed their presence, and tells Lord Garmadon to find them before they can reach the Temple of Light.
Dr. Julien and Nya begin building new vehicles for the Ninja: a power drill for Cole and a robot for Kai. As the Stone Army searches the island and Sensei Wu, Misako, Dr. Julien and Lloyd guard the hidden Bounty, the Ninja infiltrate Lord Garmadon's camp, only for Zane to rush off when he notices his Falcon. He retrieves it, but is spotted and the other Ninja have to save him. Running from the army, they narrowly escape and go back to get the machines. On the bright side, Jay was able to find the Temple of Light by aligning three lights with the holes in the medallion - the temple is at the top of the island's highest mountain.
With their new vehicles, the Ninja head for the Temple of Light, barely keeping ahead of the Stone Army. Inside the Temple, they find pictures on the walls depicting their journey from the past until the present. Further in is a great bell, hanging above a strange design on the floor bearing the Ninja's symbols. Realizing that it's the Instrument of Peace, Lloyd strikes it, causing a light to shine on him and beams of energy to reflect off crystals in the walls. Soon, the entire room is crisscrossed with beams, and one hits a pillar, making it glow brightly. At the foot of the pillar, Kai's armor transforms, and a Dragon Sword with the power of Fire appears in his hand.
In rapid succession, Zane, Cole and Jay undergo similar transformations, regaining their powers over Ice, Earth, and Lightning, respectively. As their swords manifest blades representing their respective elements, Lloyd rises into the air. The Ninja use their swords to send their elemental powers to Lloyd, who glows brightly as a golden dragon appears for a split second. When the light fades, Lloyd lands on the ground, wearing a new suit similar to the other four Ninja, and with his true powers unlocked.
The Stone Army finally marches into the Temple, but the Ninja are more than ready for them - using their new elemental powers, they easily trounce the warriors. Kai beats up some soldiers within a ring of fire, Jay electrocutes a whole line of enemies with a single touch, Zane tricks a group of his foes into turning themselves into an ice pillar, and Cole swallows his opponents in a mound of dirt. Finally, Lloyd summons the power of the Golden Dragon, creating a brilliant light that frightens the remaining stone soldiers into retreat.
Lloyd's powers cause a golden dragon to appear on the roof of the Temple, roaring mightily. From the Bounty, Sensei Wu and the others celebrate, knowing that their friends have succeeded. Atop the mountain where the Celestial Clock resides, Lord Garmadon comments that the Stone Army isn't as invincible as they thought. The Overlord is unfazed, telling Lord Garmadon that their strength grows along with the Ninja; the Ultimate Weapon will be completed just as the Celestial Clock reaches the end of its countdown. The Overlord assures Garmadon that the Ultimate Weapon will ensure that nothing will prevent the triumph of darkness, as the Celestial Clock's hands get ever closer to the skull emblem marking the time of the final battle.
Back at the beach, Dr. Julien repairs the Falcon, while the Ninja celebrate their restored powers by shooting down coconuts. The party is interrupted by Sensei Wu, who chastises the Ninja for their unseemly mirth; they may have the power to defeat the Stone Army, but the Celestial Clock is still counting down to the final battle between light and darkness. At that, Misako reveals a way to at least delay the battle: if the Helmet of Shadows is returned to its pedestal, the countdown might stop long enough for them to gain an advantage. Risking everything, the Ninja disguise themselves as Stone Warriors and escort Misako to Lord Garmadon's camp. As General Kozu takes Misako to his master's tent, the disguised Ninja are put to work carrying Dark Matter to the superweapon. The weapon is surrounded by a wooden wall, but the Ninja notice one protruding detail—a very large cannon—and ponder what Garmadon plans to attack with it.
Meanwhile, Misako appears before Garmadon, who notes that the Stone Army would never be able to catch her—unless she wanted to be caught. Using her husband's lingering affection for her, Misako convinces Garmadon to remove the Helmet, allowing her to steal it. At the same time, the Ninja are discovered when Cole attacks a Stone Soldier, forcing them to fight their way back down to the entrance as Misako rejoins them.
Before the group can flee, an enraged Garmadon stomps onto the scene, piloting a massive, four-armed robot that proves invulnerable to the Ninja's new elemental powers. Luckily, Nya arrives in the Power Drill just in time, explaining that the repaired Falcon saw that they needed her help. The Ninja make their escape with Misako and Nya, but the Stone Army pursues them until the Overlord reminds Lord Garmadon that the Ninja could turn the army against him if they don the Helmet. Unknown to the villains, Jay has done just that, only to quickly remove it when the others point out that he could be corrupted by the dark headgear.
When the Power Drill emerges in the jungle, Garmadon is quick to pursue. After a frantic chase that ends in the Power Drill being disabled momentarily, Garmadon goes for the kill, only for Lloyd to blast it with his powers. Lord Garmadon emerges from the wreckage, weakened and vulnerable; from the Power Drill, the Ninja encourage Lloyd to finish him off. Despite everything at stake, the Green Ninja is unable to strike the fatal blow, forcing him to jump aboard the Power Drill as the Ninja make their escape from the advancing Stone Army.
At the Celestial Clock, the Ninja meet with Sensei Wu and desperately look for the Helmet's pedestal with minutes to spare. As the Stone Army arrives, the Ninja find the pedestal and replace the Helmet, but it's one second too late; the countdown has ended and the final battle is upon them. As the clock fires a mighty energy flare inland, the Stone Army captures Nya and the Ninja are sent down into a crevasse. Surviving the fall, the Ninja head off to prepare for the final battle, with Jay angered at Nya's capture and Lloyd ashamed of his hesitation. Meanwhile, Lord Garmadon sees the laser aimed at his camp, and demands to know what is going on. The Overlord tells him that their superweapon is complete and his to command. The two villains return to the camp as the energy from the clock forms a sphere, completing the ultimate weapon of the forces of darkness: the Garmatron. Lord Garmadon declares that it's more beautiful than even he could imagine, and joins the Overlord in laughing in anticipation of their imminent victory.
Lloyd was still dejected over the prospect of fighting his father, but Sensei Wu reminded him that it was his destiny as the Chosen One—all of Ninjago depended on his victory. Misako added that Lord Garmadon is just as reluctant at the prospect of battling his son, and the other Ninja pledge their assistance in the final fight. Reinvigorated by his friends' support, Lloyd led the charge on Lord Garmadon's base camp, only to find it deserted. Realizing that Garmadon plans to use his ultimate weapon to corrupt Ninjago itself with darkness, Lloyd resolved that they can't let Lord Garmadon fire a single shot.
With the other Ninja battling a Dark Matter-corrupted Nya, Lloyd, Misako, and Sensei Wu ran to the shores of the Island of Darkness, where Lord Garmadon was preparing to fire his first shot. They begged Garmadon to reconsider his path, but he insisted that the only way they can be together again is if he corrupts the entire world with the same evil that has consumed his being. With the Garmatron warming up its main cannon, Lloyd jumped aboard to confront his father; however, General Kozu pinned him down long enough for the Garmatron to fire. Lloyd attempted to summon his powers to break free, but Lord Garmadon activated a trap door that drops both the Green Ninja and the Stone General out of the Garmatron.
With more of Ninjago being darkened by the moment, Lloyd lamented his failure, but Sensei Wu assured him that he did his best. Moments later, Lord Garmadon underwent a gruesome transformation as the Overlord began manifesting in the mortal realm again; Sensei Wu explained that the Overlord has possessed Lord Garmadon's body. Misako warned her son that the Overlord will show no mercy, but the recently-arrived Ninja offered their support once again - with renewed determination, Lloyd led them in attacking the Stone Army.
Lloyd himself leaped atop the Garmatron and challenged the Overlord to battle. The Overlord knocks Lloyd off of the tank. Their battle continues on the beach, briefly clashing with energy beams before Lloyd dodges and blasts his foe into the jungle. The Overlord quickly recovers and flies above the trees, delivering a brutal tackle that sends Lloyd flying. The Overlord gloats that he can keep this up for eternity, but Lloyd is alone—in response, Lloyd removes his mask and asserts that his father will never hurt him. Lord Garmadon briefly asserts himself from within the Overlord, begging Lloyd to stay strong—the Overlord's confusion and shock gives Lloyd an opportunity to take the offensive. As they clash with their energy beams once more, Lloyd calls out to his father, whose struggles cause the Overlord to falter. As Lloyd pushed his power to the limit, the Overlord roared that his father was gone. This remark unnerved the Green Ninja for a second, leaving him defenseless for the Overlord's next strike. He was quickly trapped in a sphere of dark energy by his foe and hurled him across the beach, knocked unconscious by the fall.
Later, Lloyd awoke and asked if he won as he struggled to his feet. Wu informed him that while he had been defeated, he was still alive. As the Green Ninja stumbled about confused about the prophecy, he noticed a plank for the Bounty with the symbol for "destiny" inscribed on it. Lloyd notes to the others that while they lost the fight, they haven't yet lost the battle.
Although Lloyd's injured leg was bandaged by Dr. Julien, he was still left with a noticeable limp as he regrouped with his disheartened allies. He encouraged them to keep fighting, despite the hopelessness of their situation, and succeeded in restoring the heroes' morale just in time for the Falcon to arrive with new information.
Hitching a ride on Kai's Fire Robot, Lloyd and his friends returned to the Temple of Light, where they activated a hidden mechanism that revealed the Golden Mech. When Lloyd sat in the cockpit, his powers as the Chosen One restored the ancient machine to fighting form. With the Ultra Dragon's arrival to the Island of Darkness, the group was able to return to Ninjago City, only to find it infected with Dark Matter and ruled by the Overlord, now restored to his monstrous true form.
While his allies drew the Stone Army's fire airborne, Lloyd charged the fortress from ground level and burst through the outer wall with the Golden Mech. He was quickly brought down by Nya, forcing the Ninja to drop down to aid him against the Stone Army. Despite their fighting prowess, the heroes were almost overwhelmed by the Stone Army, only to be saved when Dareth donned the Helmet of Shadows and took command of the ancient soldiers.
Lloyd proceeded to ascend the tower with the other Ninja, only to watch them fall victim to the Overlord's corruption. With his last ally -Kai- occupied with distracting Nya, Lloyd was forced to limp up to the top of the tower alone, where the Overlord was waiting. Despite the seemingly-impossible odds, Lloyd boldly challenged the dark dragon, creating a shield of energy to block the Overlord's dark flames. Summoning all of his strength and resolve to win, Lloyd unlocked the full font of his hidden powers, becoming the Ultimate Spinjitzu Master.
In his newly-empowered form, Lloyd proved to be a match for the much larger Overlord, blocking his enemy's blows and retaliating with mighty punches and kicks that sent the beast flying off the tower. To pursue the Overlord, Lloyd summoned the Golden Dragon, which he used to carry the Overlord high over Ninjago. Infuriated, the Overlord enveloped Lloyd and his mount in a massive sphere of darkness before attempting to eat them, but Lloyd concentrated his powers within the dragon's mouth, releasing an explosion of light that obliterated the Overlord.
In the aftermath of the Overlord's defeat, all of his creations and corruption vanished. Lloyd reunited with his allies in the crater left by the Garmatron's disappearance, but his jubilation was muted by his sorrow over the apparent loss of his father. No sooner had Misako comforted him, however, did Garmadon himself reappear, purified of both the Overlord's possession and the Great Devourer's venom. After a moment of bewilderment, Lloyd happily welcomed his father back, before leaving with Garmadon and Misako to catch up on the family bonding time that had been denied for so long.