Ben, Gwen, and Kevin are forbidden to fight against the Highbreed threat by Magister Prior Ghilhil of the Plumbers, who doubts the Highbreed are even as much of a threat as they claim. However, all three sides find themselves working together when Mike Morningstar, now going by Darkstar, captures all but Gwen to feed his powers. With the help of the DNAliens, Gwen frees her friends and Mike is captured while the Highbreed Lord and the DNAliens escape. In gratitude, Magister Ghilhil makes the team Honorary Plumbers so they can defend the Earth legally and help the world.

While the team fights a Highbreed commander, Kevin accidentally activates a portal, zapping Ben and the commander into the stream. There, Ben and the Highbreed are teleported to a desert planet, forcing them to team up to find a way back.

An alien impersonates Ben with hopes of using his Omnitrix to annihilate him.

Gwen forces Kevin to take her to her school's dance, forcing a clueless Kevin to seek advice from Ben. However, Ben has his own problems, as Big Chill takes over his body with each transformation and starts trying to eat every metal object in sight. Joined by Julie, Gwen and Kevin manage to subdue Big Chill, only to discover that Big Chill was only building a nest for eggs he had laid. The eggs hatch into infant Necrofriggians, and Kevin teases Ben about being a "mother." Julie takes Ben home on her motorcycle, while Gwen and Kevin miss the dance, and decide to dance to the music in Kevin's car.

Kevin, Gwen, and Ben destroy a teleporter they were working on and need help repairing it. Kevin suggests Cooper, the young boy who had helped the Tennysons in the past (who also happens to have a huge crush on Gwen). Unfortunately, Cooper has been kidnapped by the DNAliens. They track him to the abandoned military base where Paradox built his time machine. They discover that the Highbreed have erected a cloaking field, built by Cooper over the area, concealing a mysterious arch-like device. They free Cooper and have him destroy the cloaking generator, during which he has visions of the arch acting as a gateway for a fleet of ships and the Earth being destroyed. Despite destroying the generator, the Highbreed manage to repair it and continue their operations unhindered.

Forever Knights' scientist Dr. Joseph Chadwick sends Sir Morton to kidnap Ship so that the Forever Knights can use him to mass-produce a fleet of interstellar spacecraft with which to attack the homeworld of the alien dragon that escaped them. Joined by Julie, who has been taking care of Ship, Ben, Gwen, and Kevin mount a raid on the Forever Knights' stronghold to rescue him. Though Chadwick is using a control device to make Ship obey him, Julie is able to convince Ship to resist. The Forever Knights' stronghold is destroyed, and the group now has access to a spaceship since Ship can transform into the vehicle the Forever Knights had hoped to mass-produce.

While fighting one of the Highbreed, Ben's parents catch him transforming into Swampfire. They forbid him from using the Omnitrix, forcing Kevin and Gwen to fight the DNAliens by themselves. After trying to sneak out as Echo Echo, Ben gets grounded and is made to spill the beans about Gwen, getting her grounded, leaving Kevin alone. Kevin's trouble with the DNAliens eventually pushes Ben over the edge, and he breaks out of his house as Humongousaur in front of his parents to help. After a short battle aboard a small freighter carrying a rare isotope which the DNAliens plan on using, Ben's parents come to the rescue, admitting that they are proud of Ben and understand what he needs to do.

After Gwen receives an S.O.S. from Helen, Ben must go into the Null Void to save her and Manny. Once there, he must find The Wrench in order to stop D'Void, who happens to be Ben's old enemy Dr. Animo.

The team rescues a man named Tyler, who stole the Oscillator Key for the Highbreed's hyperspace gateway. He crashes his truck and suffers memory loss as he escapes. Both the DNAliens and the team track down the device, resulting in a battle. The team is victorious, but they discover that Tyler is actually a DNAlien, having managed to resist the Xenocyte controlling him. More DNAliens arrive to reclaim the Oscillator Key, capturing Tyler during the struggle. Ben opts to save Tyler instead of retrieving the Oscillator Key, and uses the Omnitrix to restore him to human form. As the DNAliens escape, the four now know their plan and prepare to take action.

The prince of the Arachnachimps, Simion, needs help in retrieving a crystal which is the symbol of the monarchy on his planet. The crystal is being kept in a base on the moon. Ben offers his help, but Kevin and Gwen are skeptical. In the midst of the battle, Ben discovers that Simion has been lying, and that the crystal is actually powering an intergalactic communications station. By stealing it, Simion will prevent Earth from calling for help against the Highbreed invasion. Ben tricks Simion into stealing a worthless acid dispenser instead, resulting in Simion having a very unpleasant encounter with the Highbreed that employed him.

A DNAlien mining operation uncovers an alien spacecraft, from which a large, alien child is released. She wanders around the nearby town collecting random items, eventually attracting the attention of Ben, Gwen, and Kevin. After a short battle, they realize that the alien is a child. She perceives Gwen as an Anodite and hangs on her every word. Needing to return the child to her parents, the team follows her back to her ship. After defeating the DNAliens, the team wakes the child's parents, who depart the planet after Ben explains that they've been in stasis for fifty years.

Paradox and Azmuth arrive on Earth to warn Ben of the approaching Highbreed fleet. Gwen and Kevin gather all the allies they've met to counter the threat. Meanwhile, Azmuth reveals to Ben that the Omnitrix contains the DNA of every sentient species in the galaxy, over one million in total, and unlocks the Master Control so Ben can effectively combat the.

Ben goes to the HighBreeds' world in an attempt to stop their attack on Earth.

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