Commander ApeTrully is captured by the Rabbit King Jumpy Ghostface while trying to make peace with the rabbits. When Mighty Ray and Mystique Sonia get captured, Lin Chung comes to the rescue.

During a time of great doubt, Lin Chung is reunited with his martial arts master. Now in spectral form, Tien Khuan gives Lin Chung three fighting tasks. As he battles Firefly King, Rhino King and Shark King -- the forces of air, earth and water -- he learns to use a new power.

Lin Chung's Harmonic Energy comes in handy when he's pitted against Hidden Kingdom's most powerful enemy. TwinMasters, a terrifying force of chaos incarnate, is a foe bent on bringing First Squad to its knees and ultimately destroying Big Green.

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.

The Zebra Brothers have stolen a magical amulet from the Owl tribe. First Squad chases the bad boys down, but just as they were in reach, their turtle mounts poop out. Back at base, ApeTrully offers the turtles a much-needed break, but Mighty Ray, still infuriated, hurts their feelings. Feeling unloved the turtles leave and fall into HighRoller's hands.

While First Squad searches for the turtles, Mighty Ray trips and swallows a turtle egg, gradually turning him into a turtle. When First Squad is forced to battle their own turtles, Mighty Ray is able to speak their language and bring them back from the brink. He eventually coughs up a baby turtle and gains a special place in the turtles' hearts.

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.

When HighRoller and his Fying Fish minions steal Mighty Ray's magic eyeballs during an attack, Hidden Kingdom is in grave danger. TwinMasters uses their powers to create a storm of unequalled chaotic energy. As First Squad deploys, team members are amazed to learn that Mighty Ray is highly adept at fighting blind; he's done it before.

ApeTrully must lead Mighty Ray and First Squad deep into the Monkey King's temple, reveal the true source of Mighty Ray's fantastic orbs and seek assistance. The Monkey King shows Mighty Ray how to "see" out of his eyes when they are used by TwinMasters. First Squad quickly finds TwinMasters' hiding place on Mt. Hima, but in order to beat their enemy, Mighty Ray must risk going blind... forever.

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.