11-year-old Ben Tennyson faces off with a new enemy, a red Galvanic Mechamorph, Malware. Five years later, Kevin and Gwen leave when Gwen takes early enrollment in an Ivy League college, and Kevin moves to be near her. Ben is forced to fight crime alone, but Grandpa Max (Magister Tennyson – the commander of the Earth-base's Plumbers) gives him a new partner, rookie Plumber Rook Blonko. Ben and Rook end up in their first team-up when Mr. Baumann's store is targeted for destruction by three alien criminals (Bubble Helmet, Fistina, and Liam) as part of their protection racket. An intergalactic hunter named Khyber watches Ben from the shadows.

Omnitrix alien debuts: Four Arms (11-year-old), Feedback (11-year-old), Lodestar, Spidermonkey, Cannonbolt (16-year-old), Bloxx (16-year-old)

After stopping Bubble Helmet, Fistina, and Liam from blowing up Mr. Baumann's superstore, Ben and Rook discover an underground alien city named Undertown where they discover that Psyphon is behind the protection racket. At the same time, Khyber sends his pet in the form of Buglizard to hunt Ben.

Omnitrix alien debuts: NRG, Water Hazard, Terraspin, Armodrillo, Shocksquatch

The Megawhatts that Ben fought in his youth come back. This time, they need Ben's help when they are being used as a power source for the villain Fistrick and his gang.

Infiltrating the Plumbers' base, Khyber downloads footage of young Ben's encounter with a corrupted Mechamorph named Malware. This shows Malware's origins and Ben's first encounter with him when he attacks Galvan Prime.

Ben meets an alien con artist named Professor Blarney T. Hokestar whose miracle elixir is extracted from a small alien called a Screegit that is kept in his lab. When a Florauna activist named Pax convinces Ben to help him free the small alien from Hokestar's lab, chaos ensues when the nitrogen in Earth's atmosphere turns the exposed Screegit into a giant, acid-spitting monster with Ben having to keep it from wrecking the city.

Dr. Animo has escaped his Plumber prison, and Ben and Rook must track him down before he transforms the world into his personal mutant ant farm.

Omnitrix alien debuts: Diamondhead (16-year-old), Echo Echo, Rath, Crashhopper

Argit and the Vreedle Brothers are fighting for possession of a doomsday device. Ben uses the almighty Alien X's godly abilities to fully recreate the universe.

Ben and Rook come across elastic, hot-blooded aliens that plan to activate a volcano with a nuclear bomb engine. Ben later falls for a female alien named Esther.

In flashbacks, it is revealed that during a fight with 11-year-old Ben, Malware touched the Omnitrix symbol on Four Arms. After the battle, he went to Dr. Psychobos and made him create a prototype Omnitrix, the Nemetrix. Dr. Psychobos plans to create the Nemetrix so that he can best his rival Azmuth and prove that the Cerebrocrustaceans are far much smarter than the Galvans. In the present, after a heated argument, Ben and Rook go their separate ways giving Khyber his best chance to capture Ben. After a long battle, Ben is forcibly changed back into his human form and supposedly falls unconscious.

Omnitrix alien debuts: Stinkfly (16-year-old), Ball Weevil (16-year-old)

Khyber tells Ben that he needs different alien DNA to complete the evil incomplete version of the Omnitrix, the Nemetrix. He also reveals that Dr. Psychobos assigned him to hunt down various species for DNA to transfer it to the Nemetrix and also tells Ben that the reason Dr. Psychobos is creating an evil Omnitrix is because of the orders from Malware. After Ben breaks free, a brawl breaks out leaving Khyber the victor. Rook breaks in and saves Ben and the duo then reveals to Khyber that they orchestrated the whole 'fight' at Undertown and Ben only let Khyber capture him so he can lead them to his ship. Ben and Rook accidentally crash Khyber's ship eliminating the DNA to complete the Nemetrix. Khyber and his dog emerge unharmed as Malware and Dr. Psychobos arrive.

Omnitrix alien debuts: Humungousaur, Big Chill (16-year-old)

While Khyber struggles to control his dog's transformations, Dr. Psychobos tells Malware that he will need a part of the Omnitrix to fix it. This causes Dr. Psychobos to infiltrate the Plumber's base on Earth and steal a part from Ben's Omnitrix causing it to malfunction. The malfunctioning of the Omnitrix causes its powers to leak into Psyphon, Bubble Helmet, Fistina, and Liam giving them abilities very similar to the Omnitrix aliens.

Gwen and Kevin pay Ben a surprise visit; a Tetramand princess and her father's fleet of warships threaten the Earth.

Magister Patelliday is captured by pirates.

Ben and Rook must stop Trumbipulor from gaining absolute power. Yet the main plot occurs when Blukic and Driba set out to find a Mr. Smoothy's after seeing an advertisement for their new grasshopper smoothies and have many misadventures along the way with one of them tying into fighting Trumbipulor's robotic rats.

Ben and Rook are attacked by Khyber and his dog (which can now transform at will without Khyber's whistling) at the Old Bellwood Days Festival. In a flashback, it is also revealed how Malware had obtained his current mutated Galvanic Mechamorph form.

Omnitrix alien debuts: Brainstorm

An old rival of Ben Tennyson named Billy Billions turns Ben and Rook into kids again while bringing Dimension 12 robots to Earth and controlling them.

Eon returns and switches Ben's mind with his younger self as part of a plot to take over the timelines. It's up to Paradox, and the two Gwens from the past and present, to help the Bens' regain their rightful minds and help to defeat Eon.

Ben takes Blukic and Driba to look for the 23rd Mr. Smoothy restaurant. After, Ben, Blukic, and Driba enter the 23rd Mr. Smoothy restaurant that keeps disappearing, they find it run by Professor Blarney T. Hokestar who is using a dimensional device to move the restaurant to different dimensions. In one dimension, Ben meets an alternate version of himself who is very rich, names his aliens differently and has lost his beloved Grandpa Max.

Omnitrix alien debuts: Feedback (16-year-old), Murk Upchuck

After Ben accidentally destroyed Mr. Baumann's car during his fight with Psyphon's minion, Thunderpig, Mr. Baumann orders Ben to make deliveries for him without using the Omnitrix. When Ben unknowingly gets the Dwarf Star (a massive power source that was going to be sold at Psyphon's auction) in his possession, Ben must fight off Pysphon, Fistina, Zombozo, Trumbipular, the Vreedle Brothers, Fistrick, Vulkanus, Sunder, and Seebik to keep them from getting absolute power.

Step up 3 free. Push comes to shove and Moose ends up in the middle of the action battling it out (unknowingly) with a member of a well-known dance crew member from the House of Samurai.

The Faction infiltrates a Galvan museum and try to take Azmuth but instead he teleports Ben and Rook to the museum. Khyber and Dr. Psychobos have a fight and Zed turns to Vicetopus and takes Dr. Psychobos. Ben reveals when he was 11, he had a fight with Malware and he took Feedback out from the Omnitrix and killed him. Angered, Ben puts his Omnitrix into Malware and he seemingly perished from the overload. Khyber takes the Nemetrix from Zed and mysteriously escapes. The group arrests Dr. Psychobos, who warns Azmuth that the planet and his species are about to become extinct. Galvan Prime's moon, Galvan B, explodes with everyone shocked and surprised.

The Gourmand Queen is captured by Incurseans, forcing Ben and Rook to rally her feuding subjects to save her.

Princess Attea springs Dr. Psychobos from prison to help her lead an invasion of Revonnah.

Incurseans take control of Earth, so Rook and the Plumbers must stop them, while Ben is somehow missing.

Ben, Rook, Gwen, and Kevin must find a solution to stop the Incurseans once and for all.

With Plumber agents trapped in Incursean territory, Ben and Rook must employ the services of Rad Dudesman, the roughest, toughest smuggler in the galaxy.

Dr. Animo remembers the time he had taken control of the Plumbers Headquarters inside Mount Rushmore with bugs that easily hack computer codes, planning to mutate everyone on Earth into grotesque, monstrous creatures resembling him.

Octagon and Rhomboid Vreedle decide to prove themselves to Ma Vreedle by pulling off successful crimes; to ensure success in numbers, they take a Pretty Boy Vreedle to assist them under the belief that Ma won't notice one out of the several others missing. When Ma does discover this, she threatens to blow up the sun if the Plumbers don't find Pretty Boy. Meanwhile Ben tries to hide from his mom so he won't get seconds on the dinner that he hates.

While attending an intergalactic auto show on Khoros, Kevin, Rook and Argit run into OTTO, an old enemy of Kevin and Argit that stranded them alone in the Null Void. But OTTO and Violent Offenders end up stealing some of the most expensive cars, and OTTO turns into a giant robot, leaving Ben having to stop him.

Albedo (who is disguised as Ben) seeks a device that will finally change him back into his Galvan form. Meanwhile, Ben (who has been disguised as Albedo by Khyber) is locked in Plumber HQ prison. It reveals Khyber has disguised Ben and Albedo as each other for their plan to work. Meanwhile Argit claims to be the hero of Undertown after stopping the Way Bads in 'The Frogs of War'.

After Ben falls for Albedo's trap, Grandpa Max and Rook search all over the galaxy looking for Ben. Meanwhile he's been secretly trapped on Khyber's hidden personal hunting preserve fighting Khyber's new pet that now wears the Nemetrix. But as Ben finds a way out, he has to deal with Albedo. When Grandpa Max and Rook arrive, they find that Albedo and Khyber have Azmuth as their captive.

Albedo took out Azmuth's brain through his cerebral vortex. With assistance from Gwen and Kevin, Ben, Rook, Max and Azmuth (whose supreme intelligence has been diminished) and the Plumbers must find a way off Khyber's Place, to get back to Earth and stop Albedo and Khyber from taking over the galaxy by absorbing Azmuth's brain sphere.

Omnitrix alien debuts: Atomix

Ultimatrix alien debuts: Ultimate Arctiguana, Ultimate Gravattack

Ben, Rook, and Max have their hands full when Phil returns as a half-human half-Terroranchula creature as a side-effect of using the Nemetrix five years ago, and starts absorbing all of the electricity and lightning in Bellwood. But when he heads into Undertown's mini power-plant and starts to absorb the Megawatts, they must find a way to stop him.

After Gwen as Lucky Girl beats Punchinello, Ben and Rook visit her and Kevin at college, but Darkstar (disguised as student Dante) gets revenge by using Charmcaster's rock monsters, and creates a cult in order to use Gwen to open up a portal to Ledgerdomain to absorb all the mana to become even powerful.

Ben's childhood crush, Kai Green, asks Ben and Rook for help when her grandfather is kidnapped by the Forever Knights who are after a mysterious sword all the way in London hidden in a secret room under the river.

Dr. Animo from the future return to the present to break his past-self out of prison, and to steal something from the SACT so that they can populate and rule the Earth with mutant animals. In order for Ben and Rook to stop him, they get assistance off someone from the future currently known as Chrono-Spanner.

Zs'Skayr and his allies awaken the great evil Lord Transyl, where he asks to make an alliance to rule the universe, but just as they team up, they manage to hypnotize everyone on Anur Transyl, and Ben's team. Now with Ben's newest alien Whampire, Ben and Hobble must discover a way to defeat Lord Transyl, save everyone, and must fix their ship in order to get back to Earth.

Ben meets the ones responsible for his intergalactic TV show and the crew who makes this Ben 10 actor more famous than Ben himself. With Ben frustrated with this show on the air and taking his fame, Simian ends up hiring an alien collector known as Collectimus who turns things into training cards for his collection.

Eon and Vilgax team up and bring together a team of evil-parallel Bens, (consisting of Albedo, the black haired 'Bad Ben', the Australian-accented, Mad Max reminiscent warlord Mad-Ben, the deformed, zombie-like Benzarro and the apathetic, gothic Nega-Ben) who go after a Ben who never got an Omnitrix (No Watch Ben). Professor Paradox helps Ben Prime (the main Ben) to find a team of good Bens (consisting of Ben 23, 10-year-old 'Gwen 10' from a timeline where she got the Omnitrix and Ben Prime's future self, Ben 10,000) to fight back and save No Watch Ben. Things take a turn for the worse when Vilgax uses a Chronosapien time bomb to wipe out Ben in every other dimension apart from No Watch Ben. Before disappearing, Ben Prime gives his Omnitrix to No Watch Ben.

Biomnitrix alien debuts: Fourmungousaur, Atomic-X

No Watch Ben and Professor Paradox return to the point where the Ben 10 multiverse began: when Ben Prime first acquired the prototype Omnitrix six years ago. From there the two start to unite the good Bens to fight Vilgax and the evil Bens. After the team is put together, Paradox sends the other Tennysons who had their watches to fight and keeps No Watch Ben in the event horizon. After Vilgax destroys the multiverse, No Watch Ben returns to fight him moments after his rescue and turns into Clockwork to undo the multiverse wipeout. Clockwork sends the Evil Bens back to their respective timelines, then returns the Omnitrix to Ben Prime, and the Good Bens and Gwen take turns beating Vilgax.

Omnitrix alien debuts: Heatblast (10-year-old)

A dangerous Chronosapien named Maltruant attempts to obtain total control over the space-time continuum with the help of an old relic called the Key to Time; Ben 23 is sent by the Azmuth of his dimension to Ben Prime's dimension in order for the latter to act as a 'mentor' to the former.

With the help of Dr. Psychobos, Ben 23 and Ben Prime successfully stage a breakout and a revolution in Mad Ben's labor camp.

In a flashback to Ben and Gwen's younger days when they were eleven, Zs'Skayr returns with a plan to have his fellow Ectonurites to possess the inhabitants of Bellwood to develop a device to permanently block out the sunlight on Earth so he can colonize the planet with more Ectonurites.

Exo-Skull, Subdora and Eon attack a hidden underground cavern to retrieve a rare egg of a Time Beast. Professor Paradox and Ben 10,000 teams up with Ben and Rook to stop the Time Beast. Rook, Ben and Skurd go after the Time Beast while Ben 10,000 and Professor Paradox fight Exo-Skull and Subdora. However, a series of mistakes lead the five of them to constantly travel through time to correct their actions. Eventually the time beast is captured, but at the end of the episode, Eon delivers two Time Beast eggs to Maltruant.

Ben finally manages to rid himself of Skurd, just when he needs the Slimebiote most. Vilgax and Albedo team up to steal Malware's calcified husk to convert into a war armor for Vilgax to defeat Ben. As Ben fights Vilgax, he realizes how much he needs Skurd to help him, while Azmuth, Luhley, Blukic and Driba fight Albedo. Azmuth uses a device he made years ago which disables Albedo's Ultimatrix and frees Skurd, in time to merge with Ben and defeat Vilgax. Ben thanks Skurd for his rescue, while Luhley decides to go on a date with Driba, while having her cousin date Blukic. In space, Vilgax's stone form oozes out what appears to be a reconstituted Malware.

In the future, Ben 10,000 and Kai Tennyson are at Plumbers' Headquarters having a party for Grandpa Max because he is retiring from the Plumbers and Rook is being promoted to be in charge of the Plumbers until Maltruant, Exo-Skull and Subdora secretly attacks Plumbers' Headquarters to get the Annihilaarg and the Dwarf Star for Maltruant to become stronger. Ben 10,000 and Kai both discover that their ally Chrono Spanner is actually their own son, Ken Tennyson.