Searching the RV, Ben finds a message left by Max claiming that he is investigating renewed alien activity on Earth, and that he has the Omnitrix.
Ben consults his cousin Gwen, and the two are confronted by Magister Labrid, a Plumber who was aiding Max in his investigation before going missing.
Ben decides that they need to finish the mission, and they proceed deeper into the facility, where they encounter an army of aliens led by an enormous, virtually invulnerable Highbreed.
Ben, Gwen and Kevin, who is now alongside them, then decide to continue working together to find out what happened to their paternal grandfather.
Omnitrix alien debuts: Echo Echo, Humungousaur In search of Max's whereabouts, Ben, Gwen, and Kevin receive a Plumber's badge signal and enter the town of Grover's Mill, where local authorities are in pursuit of a Pyronite (the species of Ben's alien Heatblast) who is allegedly burning crop circles with his powers.
Ben helps Alan escape from the police, and they investigate the crop circles, which Gwen deduces are actually circuit boards spread across the whole valley.
They discover that they were created by the aliens they previously fought (known as DNAliens), which activate the circuit boards and cause a huge machine to rise and alter the weather to lower temperatures.
Gwen convinces Ben to ask out his crush, Julie Yamamoto, after she wins a tennis match, to go on a date to a nearby amusement pier.
Baz-l explains that the symbiotic Mechamorph, nicknamed "Ship," was sent out in order to find a Plumber to rescue him, and mistook Ben for one due to the Omnitrix.
Before he can follow through, Reinrassig III comes in and tells the Highbreed Supreme that this genetic recombination has allowed their species to survive.
Vilgax has already conquered ten planets via this method, using a device to absorb the powers of those worlds’ greatest warriors in the process.
Kevin decides to hack the Omnitrix in an attempt to activate the Master Control to make Ben powerful enough to defeat Vilgax, but Azmuth contacts them and warns them against it.
The team attempts to track down Way Big, the last missing alien, but Ben runs out of time and is forced to face Vilgax.
Ben is contacted by a little alien girl named Probity who asks him to resolve an ongoing war on her home planet.
Despite Kevin and Gwen’s reservations, Ben insists they travel to the planet, which they discovered is divided between two warring factions - blue and red - both of which claim that they are merely defending themselves from the other side.
Ben eventually learns that the war began over controversy about whether the aliens’ idol, Zabin, was red or blue.
Ben eventually resorts to capturing the leaders of both factions and insisting that they stop their fighting, but they escape and resume the war.
Vilgax attacks a containment facility near a star imprisoning Zs’Skayr (“Ghostfreak”), demanding that he tell him the secrets of the Omnitrix in exchange for his freedom.
Zs’Skayr complies, but betrays Vilgax upon his release, traveling to his homeworld of Vilgaxia and converting the planet’s populace into hive mind Ectonurite minions.
During the trip, the Tiffin causes the Omnitrix to transform Ben into Rath, an aggressive and short-tempered alien of the Appoplexian species.
With Ben unable to revert to his human form, Rath causes trouble throughout the journey to the Pantophage planet, including encounters with Argit, the Vreedle Brothers, the Incurseans, and Vulkanus.
Leaving the planet, the team encounters Zaw-Veenul again, and after he admits that he knew Jarett’s intention, Rath tells him to never speak to him again.
Gwen is able to convince her past self to prevent Kevin from hacking the Omnitrix, but upon returning to the present, she discovers that Bellwood has been taken over by Hex and Charmcaster.
On Galvan Prime, Azmuth is told that his greatest invention, a greater and more effective Omnitrix-like device called the Ultimatrix, has been stolen.
Investigating security footage, Azmuth learns that the thief is Albedo, who has entered an allegiance with Vilgax with the intention of defeating Ben and taking the Omnitrix.
Albedo uses the Ultimatrix to attack and kidnap Gwen and Kevin, and sends a message to Ben demanding that he face him if he wants to see them alive again.
In a confrontation, Albedo reveals that he has modified the Ultimatrix to artificially evolve his transformations into their “ultimate forms,” enormously enhancing their abilities.
Albedo transforms into Ultimate Humungousaur and easily defeats Ben, and Vilgax appears with an army of robotic bioids.
Azmuth appears before a dejected Ben, initially chastising him for his foolish decisions, but then hinting at a means of defeating Vilgax.
Elena, a childhood friend of both Ben and Gwen, as well as a Plumber's kid, returns to explain that her father has been abducted and that she needs their help.