Ben, Gwen and Kevin sit in shock as Ben's secret identity is revealed on the news. Not convinced that anyone truly cares about his secret identity, Ben decides to leave his house. Unfortunately, dozens of news reporters are there hounding him for details. Kevin suggests that Ben lay low and head to Julie's house until the whole thing blows over. Using his new Ultimatrix to transform into Humungousaur, Ben scares away the reporters and is free to see Julie.
At Julie's house, they watch as a newscaster discusses Ben's potential threat level to society. Unable to decide whether Ben is a threat or a menace, the host of the television show tells the viewers to decide for themselves. In order to cheer Ben up, Julie suggests taking a ride in Ben's new car. While driving, they come across Kevin and Gwen who have information on the person who exposed Ben's secret.
Arriving at the informant's house, Kevin cautions that this "mastermind" could be potentially very dangerous. In reality, the informant is Jimmy Jones, a young fan of Ben's adventures. Jimmy informs the gang that he runs a website that collects pictures of aliens from around the world. After noticing the Omnitrix symbol on all of the aliens, Jimmy compiled a list of their pictures. Jimmy says that he decided to reveal Ben's secret so that people would know how he has saved the world numerous times.
Gwen spots a photo of an alien that she is not familiar with and asks Jimmy where it was last located. Jimmy shows them footage of the alien attacking a top-secret NASA facility in Orlando, Florida. The gang decides to investigate, but instead of taking Ship, Kevin offers them a new method of transportation: the new and improved Rust Bucket. Kevin explains that he decked out a standard issue Plumber ship with tons of alien tech.
On the way to Orlando, the gang takes fire from military fighter jets. Kevin attacks back, ultimately sending one pilot into the air with a parachute that's on fire. Not content with sitting idly by, Ben launches out of the aircraft and transforms into Jetray. While trying to rescue the pilot, the fighter jets begin attacking Ben! Luckily, Ben is able to save the pilots life, but not without being surrounded and captured.
Gwen and Kevin flash their Plumbers' badge to release Ben from a holding cell, while an admiral explains NASA's current problem. NASA has been building its new hyper-spaceship, The Orion, for over fifty years. However, a recent string of robberies has halted production. The admiral asks for Ben's help to stop the alien creature from stealing more pieces from the ship.
When the alien arrives, the Ultimatrix detects an un-cataloged DNA signature and enters stand-by mode. Thus, Gwen and Kevin must take the creature down themselves, but not without Ben's signature of helping. The water creature puts up a good fight, but eventually the Ultimatrix scans the alien and acquires its DNA sample just in time. Ben is now able to transform into Chromastone and fight back. However, the creature blasts a shot of water at Ben and a patch of electrical wires, inevitably electrocuting Ben. When Ben wakes up, he is told that the alien has taken the spaceship's atomic-bomb engine and he needs to get it back.
Using the new Rust Bucket's technology, Gwen and Kevin are able to locate the engine underwater. In an underwater cavern, the group confronts the creature and learns of its true intentions. The creature, named Bivalvan, is repairing his ship so that he can return to his home. Unfortunately, the detonation of the engine would kill millions of people on Earth. In order to knock some sense into Bivalvan, Ben transforms into Spidermonkey. But when Spidermonkey isn't enough to take him down, Ben goes Ultimate and encases Bivalvan in a web.
With the atomic-bomb engine properly defused, Ben exits his Ultimate Spidermonkey form. Gwen notices a strange pink glow in Ben's eyes and Ben admits that his Ultimate form was rather "different." Bivalvan later reveals that he and four other alien friends were captured by an evil monster named Aggregor. Barely able to escape Aggregor's clutches, the aliens were separated when they crash-landed on Earth. Ben promises to find and return Bivalvan and the others to their home-world. Kevin says he will return the engine to NASA and Ben contacts the Plumbers to retrieve Bivalvan.
In the end, Ben is faced with his first day back at high school after his secret was revealed. Julie calms his nerves and they walk in together. Much to Ben's relief, his classmates are appreciative of his efforts in saving the world. Back in the underwater cavern, Aggregor arrives before the Plumbers and intercepts Bivalvan.