11-year-old Ben Tennyson faces off with the 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), while an intergalactic hunter named Khyber watches Ben from the shadows.

• Omnitrix aliens used: Four Arms (11-year-old), Feedback (11-year-old), Lodestar, Spidermonkey, Cannonbolt (16-year-old), Bloxx (16-year-old)

• Nemetrix aliens used: Crabdozer

After stopping Bubble Helmet, Fistina, and Liam from destroying Mr. Baumann's store, 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 aliens used: NRG, Water Hazard, Terraspin, Armodrillo, Shocksquatch

• Nemetrix aliens used: Buglizard

The Megawhatts that Ben fought in his youth come back, seeking his help due to being used as a power source for the villain Fistrick.

• Omnitrix aliens used: Stinkfly (11-year-old), Heatblast (16-year-old), Clockwork (16-year-old), Gravattack

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.

• Omnitrix aliens used: Chromastone, XLR8 (11-year-old), Heatblast (11-year-old), Cannonbolt (11-year-old), Diamondhead (11-year-old)

Ben meets an alien con artist named Professor Blarney T. Hokestar whose miracle elixir is extracted from a small alien called a Screegit 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 Screegit into a giant, acid-spitting monster.

• Omnitrix aliens used: Ampfibian, Swampfire, Wildmutt (16-year-old), Juryrigg, Grey Matter (16-year-old), Nanomech

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

• Omnitrix aliens used: Diamondhead (16-year-old), Echo Echo, Rath, Crashhopper

• Nemetrix aliens used: Slamworm, Mucilator

Argit and the Vreedle Brothers are fighting for possession of a doomsday device called the Annihilarg. The device then activates and destroys the universe, but Ben uses Alien X's abilities to recreate the universe, albeit with some minor differences.

• Omnitrix aliens used: Alien X

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 Ester.

• Omnitrix aliens used: Eatle, XLR8, Arctiguana

In flashbacks, it is revealed that after a fight with 11-year-old Ben, Malware allied with Dr. Psychobos to create a knockoff of the Omnitrix called the Nemetrix to defeat Psychobos's rival Azmuth and prove that Cerebrocrustaceans are 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 aliens used: Stinkfly (16-year-old), Ball Weevil (16-year-old)

• Nemetrix aliens used: Terroranchula

Khyber tells Ben that he needs different alien DNA to complete 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 aliens used: Humungousaur, Big Chill (16-year-old)

• Nemetrix aliens used: .Tyrannopede

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 similar to the Omnitrix aliens.

• Omnitrix alien debuts: Wildvine (16-year-old), Walkatrout, Pesky Dust, Mole-Stache, The Worst, Kickin Hawk

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

• Omnitrix alien debuts: Four Arms (16-year-old)

Magister Patelliday is captured by pirates. Hence it is Ben, Rook and Grandpa Max to save Patelliday.

• Omnitrix alien debuts: Ripjaws

Ben and Rook must stop Trumbipulor from gaining absolute power. Meanwhile, 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.

• Omnitrix alien debuts: Way Big (16-year-old), Goop

Ben and Rook are attacked by Khyber and his dog at the Old Bellwood Days Festival. In a flashback, it is also revealed how Malware obtained his current mutated form.

• Omnitrix alien debuts: Brainstorm

• Nemetrix alien debuts: Hypnotick

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.

• Omnitrix alien debuts: Ball Weevil (11-year-old), Bloxx (11-year-old)

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.

• Omnitrix alien debuts: Ditto (11-year-old), Wildvine (11-year-old), Clockwork (11-year-old)

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

• Omnitrix alien debuts: Murk Upchuck

• Hero Watch alien debuts: Freezelizard, Rollaway, ElectricYeti(also called ShockSquatch)
• Note: This episode chronologically takes place after "Showdown".

After Ben accidentally destroys 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, Trumbipulor, the Vreedle Brothers, Fistrick, Vulkanus, Sunder, and Seebik to keep them from getting absolute power.

• Omnitrix alien debuts: Way Big (11-year-old), Big Chill (15-year-old), Toepick

The Faction infiltrates a Galvan museum and try to take Azmuth, but instead teleport Ben and Rook to the museum. Khyber and Dr. Psychobos have a fight and Zed turns into Vicetopus and takes Dr. Psychobos. Ben reveals that when he was 11, he had a battle 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.

• Nemetrix alien debuts: Omnivoracious, Vicetopus

Galvan Prime's ecosystem is engulfed by Malware and Galvan Prime is destroyed. A gigantic Malware then accumulates on the surface of Galvan. Ben is absorbed into Malware and confronts his 11-year-old counterpart. They both forgive each other for the incident with Malware and 16-year-old Ben regains Feedback. There is a shower of Mechamorphs leading to Malware becoming its original size. Malware is finally defeated and destroyed by Feedback, and Kevin ends up adopting Khyber's dog.

• Omnitrix alien debuts: Feedback (16-year-old)
• Note: This episode chronologically takes place before "Store 23".

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

• Omnitrix alien debuts: Perk Upchuck (16-year-old)

Princess Attea (Strong) springs Dr. Psychobos from prison to help her invade Revonnah.

• Omnitrix alien debuts: Astrodactyl

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

• Omnitrix alien debuts: Snare-oh

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

• Omnitrix alien debuts: Bullfrag

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

• Omnitrix alien debuts: Eye Guy (16-year-old)

Dr. Animo remembers the time he had taken control of the Plumbers Headquarters inside Mount Rushmore, planning to mutate everyone on Earth into grotesque, monstrous creatures resembling him. Hence tries again in the plumber HQ.

• Omnitrix alien debuts: Eye Guy (11-year-old), Wildmutt (11-year-old), Perk Upchuck (11-year-old)

The Secret Saturdays come to Bellwood to investigate a rash of chupacabra attacks. Ben and Rook assist, finding the chupacabras have been draining aliens of their lifeforce. They soon discover that the chupacabras are being controlled by Dr. Animo, who is an old business associate of V.V. Argost. Using the alien lifeforce, Animo successfully revives Argost in a mismatched hybrid body. Now Ben, Rook, and the Saturdays must work together to turn the tables on the alliance of Dr. Animo and V.V. Argost when they plan to make an army of "Franken-Cryptids."

• Notes: The events of the crossover specials take place after the final episode of the series.

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.

• Omnitrix alien debuts: Ditto (16-year-old)

While attending an intergalactic auto show on Khoros, Kevin, Rook and Argit run into OTTO (Kevin Schon), 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.

• Omnitrix alien debuts: Upgrade (16-year-old)

Albedo (disguised as Ben) seeks a device that will finally change him back into his Galvan form. Meanwhile, Ben (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 opens claims to be the hero of Undertown after stopping the Way Bads in "The Frogs of War".

• Ultimatrix alien debuts: Ultimate Humungousaur, Ultimate Echo-Echo, Ultimate Spidermonkey, Ultimate Albedo

After Ben falls for Albedo's trap, Grandpa Max and Rook search all over the galaxy looking for Ben. Meanwhile he has been secretly trapped on Khyber's hidden personal hunting preserve fighting Khyber's new pet called Panuncian 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.

• Nemetrix alien debuts: Panuncian

Albedo took out Azmuth's brain through his cerebral vortex. With assistance from Gwen and Kevin, Ben, Rook, Max and Azmuth 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 at Billion's Tower.

• Omnitrix alien debuts: Atomix

• Ultimatrix alien debuts: Ultimate Arctiguana, Ultimate Gravattack

• Nemetrix alien debuts: Ultimate Panuncian

Ben, Rook, and Max have their hands full when Phil returns as a human-Terroranchula hybrid as a side effect of using the Nemetrix five years ago, and starts absorbing all of the electricity 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.

• Omnitrix alien debuts: Frankenstrike, Buzzshock

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

• Omnitrix alien debuts: Ghostfreak

Ben's childhood crush, Kai Green, asks Ben and Rook for help when her grandfather Wes Green (Miguel Nájera) is kidnapped by Chadwick and the Forever Knights, who are after a mysterious sword called Excalibur hidden in Big Ben London.

• Omnitrix alien debuts: Blitzwolfer

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

• Omnitrix alien debuts: Gutrot

Zs'Skayr and his allies awaken 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 fix their ship to get back to Earth.

• Omnitrix alien debuts: Whampire

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 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 (David McCallum) helps Ben Prime (the main and real 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. However, 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

• Hero Watch alien debuts: Build-A-Guy

No Watch Ben and Professor Paradox return to the point where 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 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)

• Hero Watch alien debuts: Eye Guy, Big Bug, Vomit Man

A dangerous Chronosapien named Maltruant attempts to obtain total control over the space-time continuum; Ben 23 is sent by the Azmuth of his dimension to Ben Prime's dimension for the latter to act as a "mentor" to the former.

• Hero Watch alien debuts: Speedyquick, Toolboxx, Nighty Knight, Mr. Monkey, Techno-Bubble

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

• Hero Watch alien debuts: Dino-Mighty, Freezeghost, Handy Man, Lightning Volt, Brainfrog

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 block out the sunlight on Earth so he can colonize the planet with more Ectonurites.

• Omnitrix alien debuts: Upgrade (11-year-old)

Exo-Skull, Subdora, and Eon attack a hidden cavern to retrieve a rare egg of a Time Beast. Professor Paradox (David McCallum) 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.

• Biomnitrix alien debuts: Crashocker, UpRigg, Big Chuck

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.

• Ultimatrix alien debuts: Ultimate Rath

In an twenty-year alternate future, Ben 10,000 and Kai Tennyson are 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 attack Plumbers' Headquarters to get the Annihilaarg and Dwarf Star. Ben 10,000 and Kai both discover that their ally Chrono Spanner is actually their own son, Ken Tennyson.

• Biomnitrix alien debuts: Humungoopsaur