After sneaking out of Ninjago City, Garmadon found the remaining Serpentine and won them over by demonstrating his newfound powers, recreating the destroyed Destiny's Bounty as the Black Bounty. Offering the new ship to the Serpentine, Lord Garmadon gained the allegiance of the snakes—apart from Skales and the other Generals—and led them aboard the Black Bounty.
Lord Garmadon directed the Black Bounty to the Golden Peaks, the birthplace of the Golden Weapons, where Garmadon could uncover the secrets pertaining to the power of the Golden Weapons. He also informed the Serpentine of the prophecy of the Green Ninja, explaining that he must prevent Lloyd from reaching his true potential. Chokun suggested killing Lloyd, only to be sent to the brig under Garmadon's orders who subsequently forbidding the Serpentine from hurting Lloyd. Instead, Garmadon explained that they would focus on destroying Master Wu and the other four Ninja—without his teachers, Lloyd would never reach his full potential, and Garmadon's plans could continue. Eventually, the Black Bounty arrived at the Golden Peaks, where Lord Garmadon united the Golden Weapons into the Mega Weapon.
Shortly after, the Serpentine generals (apart from Skales) joined Garmadon's cause and he proudly presented the Mega Weapon before them. However the generals began to question if Garmadon actually knew what the weapon did, causing Garmadon to note that he just didn't have anything to use it on. At that moment, a serpentine entered the bridge and reported that they had sighted the Ultra Dragon. Realizing this to be the perfect opportunity to use his new weapon, he ordered the Black Bounty to pursue. Though he tried to use the weapon to destroy, it did nothing and eventually the dragon got away.
Hastily blaming the Serpentine's poor navigation skills for ruining his shot, he retreated to his cabin to angrily ponder why the weapon refused to obey him. In the process, he stumbled upon the journal of Captain Soto, the original owner of the ship, and wished for a better crew to man the Black Bounty. This time, the Mega Weapon responded, recreating Captain Soto and his crew of pirates, but Garmadon was severely drained of energy in the process. He then realized that the Mega Weapon could only create, not destroy, shortly before being locked in the brig (along with the rest of his Serpentine crew) by the pirates. After Captain Soto's crew was apprehended, Lord Garmadon reclaimed control of the Black Bounty and escaped from the Ninja.
Now aware of the Mega Weapon's power and limitations, Lord Garmadon called his Serpentine together for a brainstorming session on how to beat the Ninja. Despite claiming that there were no bad ideas, he had several Serpentine thrown overboard for their poor suggestions (such as creating another group of pirates, recreating the Great Devourer, or making a really big ham sandwich) before hitting upon the idea of making evil mirrors of the Ninja themselves. Using spare clothes the Ninja left aboard the ship, Garmadon used the Mega Weapon to create the Bizarro Ninja and sent them to eliminate their counterparts. When the Bizarro Ninja were destroyed, Garmadon contacted the Ninjas' Ultra Sonic Raider to vow that he would get his revenge, only for Lloyd to cut the transmission with his newly-honed powers over lightning.
For his next attempt, Lord Garmadon created a false company, "Darnagom Enterprises," and attempted to destroy Dareth's dojo, where the Ninja were training Lloyd. To get the money they needed to save the dojo, the Ninja entered the annual Ninjaball Run—when Garmadon found out, he joined the race himself with the Black Bounty. When the ship's cannon fire missed the Ultra Sonic Raider (thanks to the Ultra Dragon bumping into the Black Bounty, and the Serpentine warriors failed to prevent the Ninja from refueling on the fly, Garmadon used the Mega Weapon to create a vast chasm that the Ninja would never be able to cross.
Unfortunately for him, Nya had recently installed a flight mode in the Raider, allowing the Ninja to catch up to the Black Bounty and narrowly win the race. Enraged and disbelieving, Lord Garmadon left his ship to protest the results—thereby giving Lloyd the chance to reclaim the Black Bounty with his Ultra Dragon. Still weakened from the use of the Mega Weapon, Lord Garmadon was only saved from arrest when Skales pulled up in the Serpentine Bus, forcing him to allow the Serpentine Generals back into his army in return for the escape.
Lord Garmadon led the Serpentine into the Ninjago Museum of History, where he used the Mega Weapon to revive a prehistoric monster called the Grundle. The Ninja interfered with the process, forcing the villains to retreat, but the Grundle was still revived—unbeknownst to Garmadon, the Ninja themselves had also been reduced to children as a side effect. Due to departing, Garmadon did not witness the Ninjas' confrontation with the Grundle, or Lloyd's defeat of it using a magic tea that turned time forward again. As a result, the Grundle was fossilized yet again, the four Ninja were returned to their proper ages, and Lloyd aged out of childhood.
Bent on destroying the Ninja once and for all, Lord Garmadon retreated to Ouroboros, which he apparently repaired at some point to make it livable again. While preparing his forces for a final assault, he was ambushed by the Ninja, including a teenage Lloyd. Shocked at his son's growth and improved powers, Garmadon fled, wishing that the Ninja had never existed in the first place—this gave him the idea to create a portal to the past and change the future to ensure that Lloyd would never become the Green Ninja.
Disguising himself as a Skulkin, Lord Garmadon snuck aboard the Skull Truck and deliberately prevented the skeletons from abducting Nya, intent on removing Kai's motivation to become a Ninja. On the way back to the Underworld, he overheard Nuckal commenting that he thought he saw two Kais, and realized that the Ninja of the present had followed him to the past. Lord Garmadon was in the Skulkin camp in the Forest of Tranquility when the Ninja secretly delivered Nya to the skeletons; to counter the Ninjas' interference, Garmadon sought the aid of his own past self, quickly explaining the situation and formulating a new plan.
When Past Kai saved Nya in the Fire Temple, he found himself attacked—not by his own shadow, but by the present version of Lord Garmadon. The present Ninja were forced to intervene, but Garmadon held them off until Jay suggested using the Golden Weapons of the past against the Mega Weapon. The combined energies sent the Mega Weapon into space and undid all of the changes to the past—with the present apparently changed so that Garmadon never created it in the first place.
With his Mega Weapon destroyed, Lord Garmadon pursued other means of gaining power; namely, seeking out the Island of Darkness mentioned in Captain Soto's journal. Taking the Serpentine Generals along, Garmadon rode a Rattlecopter over the Endless Ocean, looking for any sign of the island. At that point, Skales tricked Garmadon by claiming to see the island—when Garmadon went to look, the Hypnobrai General pushed him out of the Rattlecopter and declared himself leader of the Serpentine.
Ironically, Skales's betrayal led Garmadon to the object of his quest; when he came to, he found himself on the shores of the Island of Darkness. the Overlord appeared before him and led him to a large boulder with four handles, telling Lord Garmadon that this was the first step towards his true destiny. When Garmadon turned the dials, the full Island of Darkness arose from the sea, and the Overlord revealed his plans to upset the balance of the world so that Garmadon could remake Ninjago in his own image.
To Lord Garmadon's dismay, the next step towards his destiny involved scaling a series of rugged cliffs and mountains. He demanded to know why he had to prove his evil worth to the Overlord, but the enigmatic entity merely urged him onward, promising that a great power awaited at the end of the trial.
Gritting his teeth, Garmadon carried on, eventually arriving in front of a strange clock with a dark helmet on a pedestal. At the Overlord's command, Garmadon took the helmet, causing the clock's hands to begin moving—the Overlord revealed that the former would give Garmadon control over the Stone Army, while the latter was counting down to the final battle between light and darkness.
Pleased with this new development, Garmadon triumphantly announced his return to the darkened skies above.
With the Stone Army at his command, Lord Garmadon began traveling the Island of Darkness, observing the army's operations. He was confused to see most of the soldiers working in mines, but the Overlord explained that they were searching for a dark material made of concentrated evil, which they could use to build an ultimate weapon against the Ninja. Garmadon laughed maniacally at this, declaring that he liked the sound of that.
Lord Garmadon proceeded to set up a base camp where the ultimate weapon could be constructed, monitoring the Stone Army's progress on both building the weapon and mining Dark Matter. The Overlord appeared again there, warning him that the Ninja had made it to the Island of Darkness in search of the Temple of Light. Garmadon deployed his forces to capture the Ninja, only to eventually learn that the heroes had succeeded in their quest, enhancing their powers far beyond their previous limits—worse yet, Lloyd had gained the power of the Ultimate Spinjitzu Master, making him even stronger.
Atop the cliff where the Celestial Clock rested, Garmadon commented that the Overlord's army wasn't as indestructible as they had thought. The Overlord was unperturbed, claiming that their strength was also growing—the ultimate weapon would be completed just as the countdown reached zero, and then nothing would stop darkness from overwhelming the light at last.
As the Celestial Clock continued to count down, Lord Garmadon began increasing the defenses around his camp, worrying that the Ninja might try to attack him directly before the ultimate weapon could be completed. The Overlord commented that his resolve seemed to be wavering, despite Garmadon's denials. The Overlord's prodding over his reluctance to kill Lloyd eventually caused Garmadon to snap at nearby soldiers, telling them to double their effort on the ultimate weapon's development.
When General Kozu came in to report capturing a prisoner, Garmadon was surprised to see his wife, Misako. They former couple argued about Garmadon's path to evil, and the villain admitted that he had wanted Misako to see things his way so she could rule by his side. As he lamented that Misako was one of a very small number of people who could truly understand him, Garmadon realized that he had been tricked—Misako had stolen the Helmet of Shadows in a last desperate attempt to halt the Celestial Clock.
Enraged at the deception, Garmadon pursued Misako and the Ninja in a massive, four-armed robot that proved immune to anything his foes threw at him. When the Overlord reminded him that the Ninja could turn the Stone Army against him if they wore the Helmet of Shadows, Garmadon resolved to chase them down personally, conducting a furious chase through the jungle. Just when he finally had the Earth Driller in his grasp, Lloyd arrived and disabled the robot with a powerful blast.
Lord Garmadon emerged from the wreckage, weakened and vulnerable, but his son hesitated to kill him, allowing the Stone Army to catch up with the Ninja. Garmadon left the rest of the chase to his minions as he regained his strength, but eventually noticed a strange beam of energy soaring over the trees. The Overlord told him that the countdown had ended and the final battle was about to begin, leading Garmadon back to the base camp and revealing that the ultimate weapon was finally complete. Presented with the weapon—dubbed "Garmatron" by the Overlord—Lord Garmadon gleefully declared that it was more beautiful than he could have imagined and joined the Overlord in laughing triumphantly.
Shortly after the completion of the Garmatron, the Stone Army arrived before Garmadon, presenting his recovered helmet as well as a prisoner—Nya. Garmadon tested the Dark Matter on Nya, transforming her into a loyal servant. Ordering Nya to ambush the heroes if they followed him, Lord Garmadon boarded the Garmatron and set out for the coast, accompanied by the Overlord and the Stone Army.
After arriving on the coast, Garmadon ordered the Stone Army to begin loading Dark Matter into the Garmatron's main cannon, but his actual attack was delayed when Lloyd, Misako, and Master Wu arrived. Garmadon furiously denied their pleas to stop his actions, declaring that he was too far gone for any hope of redemption—the only way he could reunite with his family was to make them (along with the rest of the world) as evil as he was. With that, Garmadon activated the Garmatron's main cannon, only to discover that the weapon required a twenty-second warm-up period. Lloyd attempted to stop the countdown, and briefly grappled with his father before Kozu pinned him down, allowing the Garmatron to fire on the village of Ignacia. Trying to prevent Garmadon from firing again, Lloyd summoned his powers in an attempt to escape Kozu's grip. In response, Garmadon used a hidden trapdoor to drop Kozu and Lloyd out of the Garmatron.
With Lloyd out of the way, Lord Garmadon fired his next Dark Matter missile at Jamanakai Village, upsetting the balance of light and darkness enough for the Overlord to begin manifesting in Ninjago. It was then that Garmadon discovered the truth: the Overlord had no intention of letting him rule Ninjago. Outraged at being a pawn in the Overlord's game, Garmadon furiously insisted that Ninjago was his to conquer, but the ultimate evil simply laughed as he possessed the four-armed villain's body to begin his metamorphosis.
During Lloyd's battle against the Overlord, the former asserted that Lord Garmadon was still alive and unwilling to harm him. At this, Lord Garmadon briefly retook control of his body from the Overlord, leaving himself open for Lloyd's assault. Unfortunately, the Overlord soon regained control, completely subduing Lord Garmadon's mind and taking full control of his body.
Garmadon was thought to have been destroyed after Lloyd defeated the Overlord, as his body had been completely transformed into that of the Overlord's true form. However, Garmadon awoke amid the rubble calling for Lloyd, completely purified of evil—not only was he himself again, but the dark magic that had given him four arms and the Devourer's venom that had turned him evil in the first place had all disappeared. Amazed and overjoyed at his new appearance, Garmadon happily reunited with his family, telling Master Wu that it felt good to be free of evil at last, He was last seen walking off with Misako and Lloyd, eager to catch up on the bonding time he had missed due to his curse.