The Defenders' secret training is interrupted when an earthquake signals that the monstrously evil Megalith is breaking free. Their mentor, Professor Alnar reveals to them that their training will not be completed. They must immediately embark on a dangerous mission to re-imprison the Megalith by recovering the four Pure Stones. Before the Defenders can leave the Dojo and start on their epic quest they are attacked by a vicious Rock Serpent and must face their first full on Di-Gata Battle!

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While travelling with Adam (whom they met in Episode 2) Seth becomes annoyed at him and challenges him to a duel. While they're away, Mel, Eric, and Kara are attacked and defeated by the bounty hunter, Snare.

The Defenders come across a carnival. The circus misfits end up controlling Erik through an amulet. Mel goes to investigate and it turns out that both the circus members and Erik are being controlled by another creature.

For the first time in their lives, the Defenders find themselves on the high seas, where they discover that their Di-Gata stones don't work over water. When bandits attack the ship they are traveling on, their friendly captain proves to be more than he appears. Kara almost drowns twice, and Mel shows her Wizard of Yan powers for the first time.

A walled city held in the grasp of a ruthless dictator has a dark secret: Its own citizens are being used as energy for the Dictator's crazed ambitions. For Kara, the situation becomes personal when her Guardian, V-Moth, is taken prisoner.

Seth learns the hard way that looks can be deceiving when the attentions of a pretty girl lead the Defenders to face destruction in a village where, literally, nothing is as it seems.

Deep in the bowels of an abandoned mine, the Defenders uncover a secret destined to shake the entire realm of Rados to its foundations: The existence of a Ninth Sigil. And it doesn't take long before the evil Lord Nazmul sends his agents Malco and Flinch to claim it for the Order of Infinis. Worse than that, Kara's boots start to act up and wishes she was not so helpless and that the Di-Gata Defenders would stop treating her like a baby.

The Defenders try to find a place to rest for a while, but everyone they encounter slams their doors in their faces. Tired from their trip, the Defenders rest at an oasis, where they spot a supply convoy in need of an escort just ahead. Seth refuses to help, however, as he is sure they will be turned away again. Meanwhile, a group of bandits plots to attack the same convoy and blame it on the Defenders, again. One of them, however, is a little hesitant and looks and sounds oddly familiar. The next morning the Defenders find the convoy demolished and follow the tracks to a nearby village, where the citizens insist that they were to blame for the recent rash of robberies.

Deep inside a mountain at the roof of the world, the Defenders encounter Brim, the original carver of the pure stones, now living in self-imposed exile and under siege by the evil Guardians. The Defenders remind him of the optimism he once held for human life and he promises to make Seth a rare and precious gift - the Vitus stone.But to make the Vitus stone, they need a wizard of Yan. And all of them were destroyed. But, secrets are revealed and Mel turns out to be a wizard herself! Unfortunately,also to make it, a stone has to be sacrificed: The Nova stone. The defenders think that the Nova stone is no more, but Brim has them fooled and takes it for himself.

The Defenders close in on the first pure stone. Their quest takes them to a remote jungle village where Erik is hailed as a Shaman, thereby making him an enemy of the tribe's medicine man. As they try to gain information from the tribe about the pure stone, the defenders enter a showdown with Malco and Flinch.

The Defenders find the way to the pure stone, and eventually find themselves in a maze. Mel sees the pure stone and picks it up, only to have it practically take over her body! But when the others find her, the Dakonauts (Lord Nazmul's unstoppable robotic army) attack them! Erik and Kara take Mel to safety, while Seth distracts them using the pure stone. Later, Kara gets a sigil spirit from zad that shows her what Mel is thinking, and when the first stone is finally acquired, it is at a terrible cost. Now the goal is not just to get the rest of the stones, but to save Mel's life.

Mel and Erik have eluded their Sand Nomad pursuers and are hiding out while Mel recuperates. Seth has struck a deal with Doku, an embittered wizard who promises him the location of Nazmul's secret keep in exchange for Seth's word that he will destroy Brakus. To make sure that Seth holds up his end of the bargain, Doku reveals that he is holding Kara hostage. She has already been infected with poison of the Saviped spider. Only six hours remain before the antidote is destroyed.

On the run from Malco and Flinch and the Sand Nomads who have overrun the Dojo, Mel and Erik encounter Bo, a brash young stone slinger who tells them of a warrior cult competition being held in a nearby county. They quickly realize the trophy is nothing other than one of the prized pure stones. As Mel and Erik make their way into the heart of the enemy camp and fight their way to the trophy. After going through a portal Seth carries the gravely ill Kara into the Ban Yo swamp in search of the antidote that will save her life. Seth cures Kara by having her be stung by spiders.

Mel dreams of a long lost monastery and a pure stone hidden there. Nazmul is able to read her dream and decides that it is Mel - the possessor of such power - whose body he must have as the host for his incorporeal being. He dispatches Malco and Flinch to kidnap Mel, unaware that Brackus has stolen Nazmul's key and has gone to the monastery for his own purpose - possession of the pure stone. Brackus gets away with the pure stone, but all is not lost. The Defenders now have the key and the realization that their enemies are divided. They may be safe - for a while.

Eluding bounty hunters, Adam charms his way into the Defenders’ encampment only to steal away in the night with their pure stones. His trail leads the Defenders to a den of thieves where an arms auction is being held with the main attraction the prized pure stone. After tricking their way into the camp, Mel is captured, and the Defenders are in disarray until Adam steps up to the plate. Using the Phase stone, he frees Mel, destroy the encampment and helps the Defenders escape with the stones.

The Defenders head for the legendary Nexus - over the centuries a traditional place of healing for Di-Gata Defenders - but the Nexus is not what it seems. Kali, a shape shifting agent of Nazmul, has been charged with obtaining a body host for him. Disguising herself as the Keeper of the Nexus, she welcomes them inside. As Kara’s wizard-like powers start to manifest themselves, Kali decides that Kara, not Mel, should be the one Nazmul seeks.

Barely escaping the Nexus with their lives, the Defenders set out for the Pinnacle, an ancient Di-Gata training temple. On the way, they face the Obelisks, an army of war machines created for Nazmul by Flinch. Erik and Kara stay behind to try to stop the destruction while Seth and Mel head for the Pinnacle to hopefully cure Mel of her wizard attacks. At the Pinnacle, Seth must face Omniaxor, his father’s Guardian. When Seth brings out his guardian, Kragus, Omniaxor takes him by the arms and breaks him into little pieces. Seth then realizes that Kragus' stone never came back, therefore he has been destroyed. In this episode, Melosa completes her Wizard of Yan training and for the first time, uses her wizard powers, in which she has full control over.

The Defenders discover The 'Machine of Binding' and Erik devises a plan to re-wire the machine to enable it to draw the pure stones to it. Their plan is foiled by an attack and as Erik lies gravely ill, a strange metamorphosis is taking place within Seth. It’s a change that will affect Seth both physically and psychologically and which may affect the outcome of their mission.

Nazmul has undertaken a secret quest for immortality that sends his team to an underground palace which once housed an ancient King who is rumored to have achieved eternal life. The Defenders arrive at the palace only to unleash an ancient force that may well rival the Megalith in its ferocity. In the process they discover a secret that plants the seeds of doubts as to the rightness of their mission. Is re-binding the Megalith the right thing to do? Do they dare to defy the traditions they have been taught since their training began? Also, the king takes Kara's body for a host.

The Defenders stop to help a caravan of refugees fleeing the war ravaged countryside for the safety of the Arboth. Brackus and his Mercenaries also descend on the village of Arboth, having identified it as the source from which the pure stones were carved. Seth deserts the Defenders as they attempt to help the peaceful Arbothians repel the invaders.

The Defenders locate the third pure stone; hidden in the sacred floating city of Callisto. Mel detects the presence of the final stone on the outskirts of the city but the presence of almost invincible Guardians makes its capture almost impossible. The Defenders learn that only the Nova Stone will help them, but this stone is not in their possession.

In a surprise turn of events, Adam shows up at Brackus’ safe house with the four pure stones and Kara all tied up. Kara is grabbed and prepared for the host body transfer that will give Nazmul physical form. The Defenders suddenly charge in and Seth gets into a fight with Nazmul, who then had to take on Omniaxor. Erik runs to see if Kara is okay and Mel goes to get the pure stones. Along the way, Adam makes a final mistake, he sets Brackus free thinking he is no longer a threat. With Kara safe and the four stones in hand, the Defenders head for the place of binding, unaware that Brackus is already making plans.

The Defenders have successfully maimed Nazmul and the Order of Infinis is now in wreck. Brackus now commands the army and pursues the Defenders to the Spell Zone. Meanwhile, Mel, Kara,and Eric go into the dojo to talk to Professor Alnar, Adam and Seth stay outside of the dojo because Seth is merged with Kragus and Adam was not trained as a Defender, they talk about random things until Seth says that Mel likes Adam. Hearing this, Adam goes crazy. Seeing that Seth overdid the conversation he says "I wish I never said that"to Adam. In a shocking twist, Nazmul finds the perfect host: But it is not Mel or Kara, it's Malco. Now the Infinis Civil War and the final battle for control of RaDos rages on, with carboard tanks. However, in the process, The Megalith is freed and the Pure Stones are destroyed.

The Order of Infinis is now a wreck and the Defenders have refused to recast the spell of Binding as it would have destroyed the planet.