Tom and the others debate how to keep the dragons a secret, even as a rambunctious young “cloaking” dragon gets loose in town and pursues a friendship with a reluctant Alex.
Jun breaks the rules by sneaking a small, adorable dragon out of the Crystal Realm and bringing it home, but finds that her older brother, Eugene, has arrived and watches her every move.
Tom has to keep his mom, Olivia, distracted while Jun, Alex, and D'Angelo use a new dragon to close off a cave leading to the Crystal Realm, and prevent her from discovering the dragons.
Tom and the riders go in search of Thunder and must face a gauntlet of dangerous dragons to find their lost friend. Along the way, Tom reveals his big secret to D'Angelo and Alex.
Much to Jun's chagrin, Eugene finally discovers the secret of dragons and demands to become a Rider, but he must bond with a dragon before he's let into the group.
When the Riders discover that Magma Breather is very sick, the only way they can help is to sneak the huge and heavy dragon into the ICARIS infirmary without being caught by any of the scientists.
The parents leave for the night and tell the Riders not to bring the dragons to the surface while they're gone; D'Angelo and Eugene get locked in the hangar with the dragons after Eugene triggers a security lockdown.
Eugene believes he and Webmaster have the strongest Rider-dragon bond; Eugene's confidence in their relationship is put to the test when Webmaster seemingly abandons him for a pack of Deathgrippers.
The Riders discover that an explosion in the Hidden World injured a dragon; with their number one suspect being Sledkin, they follow her to expose the truth.
After Buzzsaw injures a water dragon, the Riders go against their parents' wishes and "borrow" a bathysphere to travel to the deepest part of the Giant Realm Sea to rescue it.
While Tom struggles with admitting his feelings for Jun, the pair find themselves trapped inside a giant tree with an anxious colony of Woodchipper dragons.
When Jun does a Tarot reading for the team, she interprets its meaning to be that the riders will disband! In an effort to defy this fate, Jun forces the group to stick together as they search for a dragon that has breached the Rakke Town eel barrier.
The Dragon riders enlist the aid of Carla and Hazel and their scientific knowledge to help them prepare for a mission to neutralize Jörmungandr so they can return him to his chamber and seal him back inside.
Tom's overconfidence turns to frustration then despair as he struggles to procure the ingredients for Gronckle Iron in hopes of building a trap to stop the World Serpent.
After a major miscalculation by Tom in 225 leaves the fate of the Realms in jeopardy, Jun and the riders rally behind Tom and Thunder to face off the World Serpent.