During a battle with the Firefly Army, Lin Chung has visions about his old master Tien Kwan, telling him to complete his training. After the battle, Lin Chung leaves First Squad and HighRoller goes to talk with his own master, Twin Masters. Tien Kwan teaches Lin Chung to discover and use new powers called "Harmonic Energy". After that, he goes to help his friends and Second Squad member Kowloon (who was filling in for him) against HighRoller, who has once again captured Commander ApeTrully. After Command ApeTrully is freed, Twin Masters appears and throws HighRoller far away for his failures and throws a negative energy ball inside the volcano making it erupt. Lin Chung realizes that he must use his new power to turn the negative into positive energy, and uses this knowledge to stop the volcano, turning it into a large purple crystal. Commander ApeTrully and Mr. No Hands decide that Lin Chung should be the new leader of First Squad. In the end, Twin Masters talks to himself about his future plans.

Woo the Wise invents a device in an attempt to cure Mr. No Hands' self tickling. It appears to succeed, and Mighty Ray struggles to think up a new name for him. The Zebra Brothers set up a trap to lure out First Squad before using their lanterns to create a Terracotta army. During the battle Mr. No Hands gradually loses control of his hands.

Mystique Sonia and Mighty Ray have a big argument after which Mystique Sonia leaves the Big Green base and is ambushed and captured by the Zebra Brothers with the Gorilla & Kangaroo Kings.

The Zebra Brothers get caught dumping garbage in the ocean by the Stingray Warriors, but they manage to frame First Squad when they are sent out to clear up the mess.

The Pangolin Queen is capturing humans to keep as pets and captures Commander ApeTrully. First Squad are sent to rescue him. Mystique Sonia tries to keep a Raccoon named Black-eye as a pet but Mighty Ray is sceptical about this because he thinks Black-eye ate his Peanut butter when it was actually Yaksha.

The Lizard King pretends to join Big Green. First squad get upset over Lin Chung's artistic impressions of them and Woo the Wise invents a 4D image creator. While Lin Chung is training outside of Big Green, however, The Lizard king uses Woo's 4D image creator combined with his freezing powers to capture First squad so he can turn them over to Twin Masters.

The Seagulls join Big Green, but the King is disappointed by his son, so First Squad take it upon themselves to train him. Later First Squad goes and battles the Flying Squirrel Army, with help from the Seagulls. In the end, Seagull Prince lures them into a tree and Lin Chung traps them in with a rock.

The Zebra brothers poison Mystique Sonia while First Squad are fighting the Wasp army. She starts to grow hair uncontrollably, so First Squad go to find the antidote from the Humbada trees that no one has ever found before. HighRoller send the Barbets to follow them. First Squad fights the Barbets and lets them join Big Green and they get the sap and give it to Mystique Sonia. Unfortunately, this causes all her hair to fall out.

ApeTrully has a nightmare about First Squad disbanding if they discover he's the Monkey King due to Crab King betraying Big Green, so he decides to wear a suit of armor instead of his usual disguise. He goes with First Squad to investigate some human disappearances caused by a group of Star-nosed moles who are covered in mud.

First Squad fail to retrieve the Owl amulet from the Zebra brothers after their turtles get tired. First Squad decide to give the Turtles a vacation, but they run away from Big Green. HighRoller uses the Owl Amulet, which combined with Twin Masters power, turns the Turtles into giant monsters while Mighty Ray himself turns into a Turtle after swallowing one of their eggs.

The Zebra Brothers use their lanterns to create a shadow monster which steals First Squad's powers and Commander ApeTrully's ability to speak fluently. They have to race to get their powers back before they are transferred to HighRoller.

HighRoller uses the Rock Caterpillars silk to create an impenetrable shell on anything covered by it and plans to use it on First Squad. Woo the Wise invents a corn machine gun, which Mighty Ray uses and accidentally destroys one of the Turtle's shells. First Squad then have to fight the Chameleon tanks which all have HighRollers new coating for ammunition.

First and Second Squad start fighting over who is best, again. First Squad is sent to fight the Flying Squirrel Army while Second Squad is sent to fight the Yaks. All heck breaks loose when Second Squad get possessed by Twin Master's chaos energy.

The Zebra Brothers trick Hamster King into fighting First Squad by making him believe First Squad harm children. Mighty Ray is ordered to be the baby turtle's babysitter while the adult turtles are away.

The Bald Eagles turn into Pterodactyls and gain the ability to turn anything they hit with the purple goop they spit into prehistoric versions of themselves. Jumpy Ghostface gets turned into a prehistoric rabbit while First Squad, the Air Force and Tank Army try to fight off the Pterodactyls.

The Zebra Brothers turn the guys of First Squad into girls and also makes their personalities more passive. They then trick the Crane King into thinking First Squad want to pluck the Crane's feathers to make dresses with.

Mighty Ray's eyes are stolen by the Flying Fish army and given to Twin Masters, who uses them to create a storm of chaos energy. First Squad return to where Might Ray first received his eyes to restore his connection to them, before they can stop Twin Masters plan: to create a deadly chaotic storm which turns anything its lightning hits into monster versions of themselves. First Squad thwarts Twin Masters plan by feeding Mighty Ray lots of bananas to overload his eyes (Just like he did when he was about to take down HighRoller one time).

The Slug King is capturing animals and humans to keep in his collection. Sparky White is captured, so Sparky Black asks First Squad to help him after HighRoller refuses to help him. When Commander ApeTrully, the tank army and most of first squad are also captured, Lin Chung and mighty Ray use come citrus fruits to dissolve the Slug King's slime he uses to hold his collected victims. After all of Slug King's collected people are freed, the Zebra brothers use their ghost lanterns to create a slime monster which traps everyone (including the Zebra brothers) in its belly except Mighty Ray and Lin Chung. They defeat it by having it trap Lin Chung so he can use his harmonic energy to protect everyone from Mighty Ray's blasts.

Mighty Ray and Crocodile King start arguing about who is better and have a competition to find out who is the best blaster in Hidden Kingdom. Twin Masters resurrects a T-Rex and a caveman to fight First Squad. When First Squad fight them, the T-Rex and the caveman become First Squad's friends when Lin Chung saves Crocodile King. However, they still have to deal with Twin Masters.

Using earwax harvested from a Giant Centipede, the Commander of Darkness transforms his minions into six-armed giants and disguises himself as the Koala King in an attempt to take revenge on First Squad when they arrive to ask the Koala King to join Big Green.

The Sword of Darknesses' location is revealed so First Squad with the Air Force have to hurry to stop it falling into the wrong hands. First Squad finds that HighRoller (without the Zebra Brothers) is trying to get the Sword before First Squad, with Beetle King as his sidekick. Ultimately, the Sword is sucked into a vortex and Beetle King joins Big Green while HighRoller is chased away by Wolf Eels.

The Commander of Darkness manages to take control of the Dragons and kidnaps Mystique Sonia. First Squad and the Air Force go to rescue her using upgraded Planes that shoot water to counter the Dragons' fire. Mystique Sonia escapes from the Commander of Darkness' clutches by charming the Mother Dragon with her flute.

Spotter the Rabbit attacks Rabbit Castle with the Mantis army to try and take the throne from Jumpy Ghostface. He demands a 1-on-1 fight with Jumpy, but First Squad turn up anyway and with the help of the Beetle army, fight off the Mantis' while Jumpy fights Spotter.

HighRoller kidnaps Fox King's Family, and commands Fox King and Spider King to attack First Squad.

After a hypnotic sound on the Octopus and Stingray King, First Squad goes and look what hypnotized them. But then they find a Lantern Fish who hypnotized the Sea Kings and captured Commander ApeTrully. While First Squad is rescuing Commander ApeTrully, Mystique Sonia is uncomfortable when they are joined by the Big Green Navy's best warrior Lady Green.

While sealing up volcanic vents in the ocean, First Squad is shrunken down to size by some Jellyfish and captured by the Zebra Brothers. Upon First Squad being brought to HighRoller, it is shown that the Jellyfish are actually tiny aquatic humanoids led by Yan Ching who have been tricked by HighRoller. When Yan Ching joins Big Green, he calls it "Little Green", to which Mighty Ray replies by correcting him, which he thinks doesn't matter. It is unknown how First Squad got back to their normal size.

Under the orders of Twin Masters, HighRoller sends the Sea Elephant Army and the Hermit Crab Army to a secret island to recover Twin Masters' heart. At the same time when First Squad and the Infantry are out to destroy Twin Master's heart, Mystique Sonia has some doubts about Yan Ching. When First Squad finds Twin Masters' heart, it is revealed to be a chaotic bomb.

The leeches invade Big Green and impersonate most of First Squad, the King of Lions and Commander ApeTrully. Only Lin Chung and Yaksha can put a stop to it.

HighRoller uses the Amulets of Chi Gong to fuse several captured Cheetahs, Oxen, and Pythons with himself, Bearstomp, and the Zebra Brothers creating his own equivalent to First Squad (who once again sides with Second Squad). As Lin Chung and Alpha Girl go after HighRoller, the others steal the Amulets of Chi Gong and fuse with each other as well. They defeat HighRoller by using the Amulets to fuse him with the Zebra Brothers, much to his annoyance.

The Seahorses, after helping First Squad to defeat Flying Fish army, join Big Green to give them special fighting abilities. But are they planning something evil? It turns out they are as HighRoller has got another Seahorse and both are feeding off their negative energy and handing it to Twin Masters.

Something really fast attacks the human village but no one has seen what. The First Squad sets out traps to find out who's attacking the humans. Meanwhile, Mystique Sonia has taken some advice from Crane King (Chanting "Power, Energy, Power") to become faster, but she continuously abuses it.

Commander ApeTrully receives a message that an unknown animal king wants to join Big Green. But, it's a trick and they are ambushed by the Bearstomp and his Bears. When First Squad fights the Bears, the Zebra brothers capture ApeTrully and bring him to the East Citadel. Lin Chung, Mystique Sonia and Mighty Ray come up with a plan to infiltrate East Citadel by using the Spirit Cave to become their inner animals (A Panther, a Swan and a Boar, respectively). Even if they find Commander ApeTrully, they also would have to fight Twin Masters who was also involved in Commander ApeTrully's capture, as well as their toughest opponent yet, Commander ApeTrully (because Twin Masters blasted him with a huge amount of chaotic energy).

Twin Masters hires the Oyster-Rahmas to widen a trench at the bottom of the ocean in an attempt to drain Hidden Kingdom's oceans. Upon enlisting Lantern Fish King's help, First Squad, Commander ApeTrully, the Sailor Brothers, Sammo the Whale, and Lady Green go underwater to stop Twin Masters.

First Squad, Bearstomp and some other people get kidnapped and are forced to fight like gladiators for a Minotaur's enjoyment. Even when they make their escape, they must navigate through the labyrinth while evading the Minotaur's minions.

After Jumpy Ghostface is zapped by Twin Masters, Jumpy's dreams start coming to life and Jumpy Ghostface's dreams are mostly about evil monsters (consisting of Moosey Ghostface and Tri-Puppy) and a dream version of Beastomp. Jumpy Ghostface banishes the dream monsters by dreaming up a giant version of himself and forcing them back to Woo the Wise's new invention that sends the monsters back to the dream world.

Lin Chung has lost his power of Harmonic energy while battling the Twin Masters after a fight with Twin Masters' enhanced Gila Monsters and speaks to Tien Kwan. Meanwhile, Twin Masters turns Polar Bear King into a Yeti and Bald Eagle King into a Phoenix so they can destroy First Squad. Lin Chung regains his harmonic energy from the other members of First Squad and uses it to return Polar bear king and Bald Eagle King to normal, much to Twin Masters' dismay.

Twin Masters controls an asteroid to crash in Hidden Kingdom. First Squad has to go to space with Woo the Wise's new invention, a space rocket.

HighRoller teams up with his old school friend (who was also a rival of Woo the Wise) to create robot versions of Groundhog King and his Groundhog Army to destroy First Squad. Woo the Wise also takes part in the fight where he duels his high school rival.

Lin Chung is lost in the forest after the Air Force's fight with Roto-Wolves. With Mr. No Hands on a mission, the rest of the First Squad has to find him now in the Roto-Wolves' forest.

Mr. No Hands trains the rest of First Squad in a forest to build up their teamwork skills. Meanwhile, Twin Masters turns ants into big ants to activate the magma inside the earth to destroy the Hidden Kingdom. Mystique Sonia and Mighty Ray get captured so the other members of First Squad must save them.

After HighRoller stole a powerful Orb from a temple, he turns himself into a Hydra so he can destroy Big Green and First Squad. Later, HighRoller thinks that with his new powerful body and powers he can destroy Twin Masters. HighRoller goes and fights with Twin Masters. In the end, Twin Masters says that the day of Wreckining is coming soon.

Lin Chung is blasted in a fire tornado by Twin Masters which sends him 1000 years in the past. In the past of Hidden Kingdom, it is revealed that Lin Chung was responsible for the rise of Twin Masters, as Twin Masters was once Prince Yang Tu, who wanted complete and total control of the Hidden Kingdom. Lin Chung tried to prevent Yang Tu from walking the path of evil. Unfortunately, instead of changing Yang Tu's fate, Lin Chung became the one that caused Yang Tu to become the Twin Masters we all know, Thus creating a time paradox.

HighRoller plans to attack Big Green with the Blowfish army, and his plan is to sink Big Green under the ocean.

HighRoller uses a transference sceptre to switch bodies with Lin Chung. While Lin Chung is HighRoller, he hears about Twin Masters' plan that the Hidden Kingdom can't unite to fight with him when he will be at his full power and it's coming soon. Will First Squad find out that Lin Chung isn't Lin Chung?

Twin Masters tells HighRoller to kidnap First Squad. While HighRoller enlists Yak King, Lizard King, and the Flying Squirrels to attack Big Green, he doesn't know that Twin Masters also got some bounty hunters to do it. When the bounty hunters successfully capture First Squad, HighRoller plans to capture First Squad from them as he will not let them take the credit for First Squad's capture.

The Swamp Hippos start terrorizing villages and blame the Dogs. So First Squad and Wu Sung have to stop them. At the same time, Wu Sung tells First Squad that his brother Dog King hasn't been comfortable living amongst humans. When First Squad defeats the Swamp hippos, the Swamp Hippo King tells them that Twin Masters put 2 chaotic gems in his mouth.

When Twin Masters plans to get the ultimate power for himself, Lin Chung feels it and tells all of Big Green about his plan. Woo the Wise remakes Big Green Base like a turtle so Big Green can both walk and shoot projectiles, hoping it will be enough to destroy Twin Masters. In the forest, Big Green is stopped by HighRoller, Chameleon Queen, the Zebra Brothers, and Bearstomp, keeping First Squad from stopping Twin Masters. First Squad goes into Twin Masters' cave but they are too late because he has broken the shell and evolved. He now has a new body and is more powerful than ever. Twin Masters shoots and destroys Big Green Base. All hopes of defeating Twin Masters are gone, until Lin Chung talks to Tien Kwan and he draws a Bronze Giant without thinking. Bronze Giant is a combination of all the heroes of Hidden Kingdom. It's Hero 108 and it has to have 107 Animal King/Queens and the Heroes of Big Green to combine it. Twin Masters starts destroying Hidden Kingdom and says that he will destroy all life and even HighRoller. After that, the Zebra Brothers, Bearstomp, Chameleon Queen, and Seahorse Prince join Big Green to form the Bronze Giant. After they have formed it, they go to finish off Twin Masters before they have destroyed the Hidden Kingdom. Later the Bronze Giant absorbs all the positive energy from Hero 108 and it causes Twin Masters. Everyone is happy and peace with the humans and animals is restored. But HighRoller, the Zebra Brothers, and Bearstomp go back to the East Citadel (a.k.a. Bear Castle) because they don't want to stay with the heroes. Commander ApeTrully then says it is time to rebuild Big Green. Tien Kwan tells Lin Chung that many challenges lay ahead for Big Green and Lin Chung tells his master that they will be always be ready.