While on their way to the amusement pier, Ben, Gwen, and Kevin encounter the Forever Knights with the use of an alien tech tracker. Kevin, Gwen, and Ben track the Forever Knights to the pier, where they are looking for a piece of alien tech buried there. On their way to retrieve the component, Ben encounters an off-world (and notably out of shape) TetramandPlumber named Gorvan. Gorvan states that his objective is to retrieve several illegal alien tech components and quickly recruits Ben, Gwen, and Kevin to complete this task. Next, the trio go to a Forever Knight castle in the forest. Ben and Kevin fight their way through the Knights and the security system, where Ben discovers the next component is hidden in a (notably chained) robotic dragon's den. After defeating the dragon, Ben retrieves the component and brings it back to the nearest Plumber base, where Gorvan very rudely takes the component for safe keeping.
Next, the team hunts down a recently uncovered component at a military base. Kevin decides to sit out through the mission after being insulted by Ben and Gwen. As Ben makes his way through the surface (fighting Vulkanus' pick axe minions), Gwen deactivates the security systems for him underground. Eventually, Ben makes his way to Vulkanus himself (who takes disappointment in that Kevin decided not to join Ben on his mission) where Ben must fight and defeat him at the ammunition range and Ben takes the component. Back at the base, after giving Gorvan the component and telling him about Vulkanus, Gorvan states that Vulkanus will have to be "dealt" with eventually. Kevin, Ben, and Gwen note that Gorvan is acting suspicious and they should keep an eye on him.
Gorvan receives a message and states it's from the rest of the Plumbers asking for a progress report. Gorvan leaves to deliver it on a encrypted channel. Next, Ben travels to a hatchery where a group of DNAliens are using the component to power an egg machine. After fighting his way through a ghost town and the hatchery, Ben retrieves the component and brings it back to the base.
After unlocking Grandpa Max's secret files, Ben, Gwen, and Kevin discover that Gorvan is a disgraced Plumber who was thrown out for hoarding and selling illegal alien tech. The revelation provokes Kevin to hunt down Gorvan without backup and Ben goes after Kevin. Meanwhile, Kevin has caught up with Gorvan, who lured Kevin into a Xenocyte hatchery inside the base. After finally catching up with Kevin, Ben finds him partially transformed into a DNAlien. After beating Kevin, Ben turns him back to normal and sends him back to Gwen. Ben continues Kevin's short-lived quest to find Gorvan and defeats him. After getting back to Gwen and Kevin, Gwen explains that the final component (which was hidden inside the base) is a sub-energy core. A Highbreed breaks in and steals the component.
Using Kevin's tech tracker, they trace the Highbreed to three now-completed weather towers. The team is immediately split up due to a swarm of DNAliens. Ben deduces that a nearby rocket ship is the control center for the weather towers and proceeds to remove it from the circuit board, despite Gwen's attempted warnings.
After fighting off a swarm of DNAliens, DNAlien hybrids, and a Highbreed, Ben makes his way to the auto-pilot where he moves the ship out of the circuitry. However, the Highbreed explains that removing the ship starts the weather towers up and gloats that if not for Ben, his plans would be ruined and tosses Ben out of his ship so that Ben can see his own handiwork in action.
The game rewinds to the beginning of the last level, where Gwen tries to warn Ben not to go into the ship. After the failed attempt, Gwen and Kevin split up to take down the towers' force fields. After accomplishing their mission, they meet with a full sized Humungousaur, who easily takes down the remaining towers. While exploring the wreckage of the towers, the team discovers that the Highbreeds are planning to make a giant arch.
Ben: Why don't we call it a day and go grab some smoothies?
Ben: (To Kevin) I thought your knowledge of aliens was linked to weapons and auto parts! What did you do, brush up against a scientist and accidentally absorb his brain? Kevin: I know stuff too! Like...well...a lot of stuff...
Kevin: (After Gwen asks "Are you coming?") Nah. I think we should all stick to what we know. You guys go fight alien bad guys and I'll just stick here and think about auto parts. (Gwen slams car door)
Spidermonkey: Oh, don't you monkey with the monkey. [makes monkey noise]