Dr. Dynamo sends a probe into Inner Earth to collect samples to research. When it returns, the crew of the Dynamo Dome are surprised as what had been thought to be three rocks, were instead three dinosaur eggs. After they hatch, Super Dinosaur takes an immediate shine to them and acts as their big brother, even housebreaking them and teaching them how to play basketball. Derek and Dexter break the news that they have to be sent back to Inner Earth.

After they leave, Super Dinosaur sulks around with no one to play with. Suddenly, he finds the three baby dinosaurs rummaging around. They escaped from the probe before it entered Inner Earth and get grow in size after colliding into a canister of Dynore gas. The three dinosaurs mutate and start causing havoc around the Dynamo Dome, ruining equipment, and foiling Erica's hope of attending a school dance with her old friends. Derek, Dexter, Erin, and Erica fail to capture the three, but before making it outside the Dynamo Dome, Super Dinosaur manages to lure them with a basketball game, where they're finally caught.

While on an Earthcore training exercise, Eliot Casey spots something strange. He tries to tell his superior officer, but is told to pack up as they're about to leave. Eliot decides to investigate on his own and finds Dino-Men with odd bumps on their bodies. Two of them ambush him and in the chase he notices his crew fly off. Fearing his father's wrath over disobeying orders, Eliot calls Derek and Super Dinosaur for help.

Derek and Super Dinosaur arrive just in time to take out the Dino-Men chasing Eliot. Derek makes a mark in the ground to indicate where the Floor Door will open, as no one's at the Dynamo Dome to activate it so it's been set to a thirty-minute timer. As he ponders how the Dino-Men got on an island Earthcore made untraceable, one of Max Maximus' ships land directly onto the Floor Door marker. Tricerachops walks out, handing food and medicine to the three Dino-Men before they tell her they've encountered humans. As the two groups clash, another one of Maximus' ships arrives, this time featuring a crew of Dino-Men and a hologram from the man himself. He derides Tricerachops for not destroying the exiled Dino Men, who suffer from defects caused by the cloning process. Maximus demands the other Dino Men kill the "freaks." Tricerachops tries to get them to stop attacking.

With the Dino-Men preoccupied, Derek, Super Dinosaur and Eliot try to devise a plan of escape. The Misfit Dino-Men appear, offering their assistance. The group create a distraction to attract Tricerachops and the other Dino-Men. They quickly realize they've been had and return to the landing zone, where they see the Misfits trying to clear the way for the Floor Door. The Dino-Men attack, with Derek and Super Dinosaur trying to fend them off. As the Floor Door opens, one of the Misfits gets hit and Eliot drags him through the portal to safety. Inspired, Tricerachops knocks out the rest of Maximus' Dino-Men, letting everyone escape.

Erica receives an acceptance letter from a creative writing program Ms. Finkle had her apply to, but her parents are too busy working on a mission to notice. Max Maximus has devised a formula to create synthetic Dynore with the use of just three ancient elements. Derek and Super Dinosaur are sent off to retrieve the items before Maximus can. However, Tricerachops and the Dino Men are able to escape with the first two elements. For the third location, General Casey sends his son Eliot alongside the two. Together they're able to take back all three elements and head to the Dynamo Dome.

Maximus and the Dino-Men take control of the Dynamo Dome, locking all human attendants in a cell. Maximus proclaims that he no longer needs to create synthetic Dynore, given the Dynamo Dome's portal to Inner Earth. Super Dinosaur, who managed to escape in the earlier frenzy, is found out by Tricerachops and captured. Noticing her earlier hesitations, Maximus demands she use the opportunity to finally end Super Dinosaur to prove her loyalty. Tricerachops refuses to destroy a fellow dinosaur and instead commits a mutiny against Maximus alongside the other Dino-Men. She then pledges to take over the world alongside her family.

Super Dinosaur's harness is removed and Maximus' arm is torn off before being thrown into the same cell as Derek and the rest of the crew. There, Super Dinosaur coughs up the key needed to exit. Maximus reveals a device of his that he can use to disable the Dynamo Dome's defense system, which have now been taken over by Tricerachops and the rest of the Dino-Men. General Casey, who broke his leg in the initial attack, is brought to the infirmary by Bruce Kingston. The remainder of the team head to the entrance of Inner Earth, which Tricerachops is attempting to open to allow dinosaurs to roam freely into Earth. The Dino-Men fend off the attackers, allowing the door to open. Derek and his father race to the control room to retrieve the three elements and devise a way to use them to close the door once again. Just as a pack of roaming dinosaurs are about to head through, Derek manages to close it. Tricerachops and Terroropterx gets teleported to a unknown location before killing Derek.

Locked up in an Earthcore cell, Maximus taunts Dr. Dynamo with more information regarding his wife, Juliana. He brags about having erased any memory of her existence from the Dynamos and that while he may be locked up, his most powerful weapon is about to be activated. On the roof of the Dynamo Dome, Erica expresses guilt to Super Dinosaur over the Maximus invasion and plans on secluding herself. Derek and Super Dinosaur are sent on a mission to stop an Earthcore ship from being attacked by Dino-Men. They're easily defeated by the duo, allowing Derek to take a gun he believes to be the weapon Maximus was talking about. They only find one person on the Earthcore ship: a boy named Tom, who claims his mother was a scientist who vanished alongside the rest of the crew.

After failing to respond to his distress call during a mission, Derek convinces his father and Super Dinosaur to head out for a camping trip to help clear Dr. Dynamo's mind. Before leaving, Erica warns Derek that the site they're going to is well known for paranormal activities. Derek dismisses it as the three went there years earlier with no issue.

Just as they're about to go to sleep, their camp is attacked by a ghost-like creature. Derek and Dr. Dynamo devise a plan to capture it, but it backfires due to Super Dinosaur's fears, leaving them trapped in a cave. There, Dr. Dynamo discovers pictographic writing that details an ancient civilization from Inner Earth called the Reptiloids. They explored the top surface through gateways they built in temples spread across the planet, eventually retreating back to their home, viewing the outer level as a wasteland.

The trio are once again attacked by the ghost lizard, but this time Derek disables it with a nearby control panel. They realize that it was a holographic defense mechanism created by the Reptiloids to protect an ancient relic. While Dr. Dynamo translates the glyphs on the object, Derek and Super Dinosaur battle against rock golems similar to those they fought in the hidden temple. Just as they're about to perish, Dexter activates the device, ending the threat. With oxygen running out and the cave starting to collapse, they narrowly escape.

Erin joins the Earthcore cadet program. Dr. Dynamo calls Derek from her going away celebration to tell him that he plans on infiltrating Castle Maximus to retrieve a storage device called the Infostar. There, Dr. Dynamo gets captured by Minimus. He calls the Dynamo Dome offering a trade: Maximus for Dr. Dynamo.

Derek and Super Dinosaur manage to free Dr. Dynamo and escape. Back at the Dynamo Dome, Bruce and Sarah call unveil a virtual reality haptic sphere that'll allow Erica to attend her creative arts classes.

After a failed attack on an underwater Earthcore research facility, Minimus replaces Squidious as the Shark Men's leader in the Lair Leviathan. Squidious is eventually apprehended by Earthcore and arrested. General Casey sends Derek and Super Dinosaur on a recon mission to locate the Lair Leviathan, as under Minimus' control it could be utilized to create great destruction.

Derek and Super Dinosaur are outnumbered by Shark Men and abort the mission. Minimus realizes that with a nearby Dynore deposit he can transform the Lair into a weapon powerful enough to break the sea floor and enter Inner Earth. At the Dynamo Dome, Super Dinosaur and Derek have no other choice than to enlist Squidious in their assault on the Lair Leviathan. Fearing what Minimus will do to the ocean, Squidious agrees to help.

Together, the three infiltrate the Lair Leviathan just before Minimus is able to transform it. Super Dinosaur, Derek and Squidious attempt to take over the control room, but Minimus tries to persuade him into joining his side. Squidious attacks Minimus and floods the Lair Leviathan, causing everyone to evacuate.

Dr. Dynamo begins teaching Erica how to use the Floor Door. After coming back from a mission with explosive Dynore mutated centipedes, Super Dinosaur is mysteriously transported to a variety of locations. Dr. Dynamo and Erica realize he's going to locations he's recently visited with Derek. Dr. Dynamo fears if Super Dinosaur cycles through all destinations, he might vanish for good.

One of the destinations Super Dinosaur is sent to is the surface of the Lair Leviathan. There, he notices that the Shark Men have excavated a Reptiloid artifact and are about to hand it over to Minimus. Derek is transported to the location and together they're able to retrieve it from the Shark Men. Super Dinosaur is sucked through a Floor Door once again, arriving at the abandoned mine shaft Maximus previously used as a base.

Thanks to Erica, Dr. Dynamo is able to discover the source of Super Dinosaur's problems. By accidentally ingesting the goo of some of the mutated centipedes, his energy signature was severely interfered. They're able to devise a plan that requires Super Dinosaur to use one of his rockets to force the Floor Door to reset its location log. Thinking their hideout has been ambushed, a nearby Tricerachops and Doometrodon attack.

Tricerachops hijacks General Casey's ship and holds him hostage with the hope of freeing the other Dino Men. Derek and Super Dinosaur fend her off, telling her that Minimus had already freed them. Disobeying advice from the Kingstons, Derek is able to stop the ship from exploding. Bruce and Sarah notes his reckless behavior, wondering if it's due to Dr. Dynamo spending so much time with Maximus.

Back at the Dynamo Dome, as a birthday present for Super Dinosaur, Derek modifies the Earthcore virtual reality training system to display Super Force Team Awesome, the duo's favorite video game. To get the game to run, he has to disable all safety protocols. Alongside Erica, the three jump into the game and quickly get hurt, realizing that they are experiencing physical pain. Wheels gets stomped by a cyclops and sustains significant damage. Erica tries to exit the game, but realizes she can't because of the safety protocols being shut off. Derek believes they can exit the game if they reach a save point, which on this level requires beating a stage boss named Croco-Gator before the timer runs out.

At a beach, Derek and Super Dinosaur confront a group of Shark Men wielding a powerful, unknown scepter. After fending them off, the two request help from Squidious, who warns that the creator of the weapons is beyond the power of land dwellers. After being denied exit, Squidious escapes from Earthcore lockup, taking a container of Dynore with him.

General Casey sends Derek and Super Dinosaur after him, where they discover an underwater labyrinth. A clan of Hammer Head Shark Men attack with the same scepter and in the conflict Derek and Super Dinosaur accidentally open an entrance into the labyrinth. Through the maze, they're able to catch up to Squidious, who saves them from a group of leeches. Squidious reveals that they're in a sanctuary devoted to the Queen Leviathan, a massive, evil force who birthed the ship he commands. To keep her slumbering, Squidious must continue feeding her Dynore. Squidious suspects his Shark Men led Minimus there to steal her Dynore reserves. A Hammer Head Shark Man attacks, destroying the Dynore Squidious brought. Super Dinosaur uses the last of his suit's energy to feed the Queen and keep her asleep.

Erin completes the Earthcore cadet training program with a record setting run, upsetting Derek as he set the prior record. To clear the air and test out some new items created by the Kingstons (including a vehicular upgrade for Wheels), Erin and Derek take on another training program. Instead, they bicker some more. After being startled by Squidious, Erin checks in on her sister, who gets annoyed by Erin's critique of her Floor Door abilities.

While doing her daily look out, Erin spots seismic activity and a Dynore deposit in New Mexico. With the adults asleep, she tries to alert Derek and Super Dinosaur, but Derek shrugs her off, feeling that if it was important General Casey would've called them. Erin decides to go on the mission with Pixie, where they're immediately attacked by a giant mutated centipede. She notices that it's following sound and is able to incapacitate it.

At the Dynamo Dome, Erica tries to apologize for earlier but finds out that her sister is gone. She wakes up Derek and Super Dinosaur and they transport to the location. In typical fashion, they come in loud, causing more centipedes to wake up and attack. After initially struggling to work as a team, the three are able to defeat the centipedes. Derek puts Erin in charge of the rest of the mission, who spots a giant Dynore stash somewhere. The trio head to a spot in the desert just as it breaks open, revealing a mutated scorpion named Scorpinox. The monster devours Dynore and is the cause for the mutated centipedes. Erin panics, but Derek is there to tell Super Dinosaur to destroy his Dynore collection. Erica calls in, telling Super Dinosaur and Derek about a new combination ability that their parents built into Wheels. They're able to get Scorpinox to fall into a pit, where he passes out. Derek says he expects them to go back to normal after losing their Dynore exposure, but says they should tell Earthcore anyway.