In The More Things Change: Part 2, Ben along with Rook, investigates Undertown. They meet Psyphon who reveals that he has started a gang. Ben battles Buglizard as Shocksquatch and with the help of Rook, defeats Buglizard and arrests Psyphon and his gang members.
In A Jolt from the Past, Ben discovers that a guy named Fistrick and his gang are illegally keeping the Megawhatts. Ben and Rook free the Megawatts and arrest Fistrick and his gang. Ben also unlocks and transforms into Gravattack.
In Have I Got a Deal for You, Ben meets Blarney T. Hokestar, a dealer and Pax, an alien right activist who claims Hokestar is illegally keeping a Screegit. This is proven true and since the Screegit reacts with Nitrogen gas, it creates trouble. However, it is subsequently defeated by Ben and Hokestar. Then Solid Plugg, assistant of Hokestar, and Pax are arrested.
In It Was Them, Ben is attacked by Slamworm, which is once again the work of Khyber. His suspicion arouses over these attacks. Later, he and Rook go to arrest Animo who has managed to escape. At Animo's hideout, Ben is once again attacked, this time by Mucilator. Eventually Ben and Rook manage to defeat the Mucilator and arrest Animo. Ben unlocks Crashhopper.
In So Long, and Thanks for All the Smoothies, Ben and Rook check out a mysterious ghost ship. which is revealed to be a Contemelia ship. Later on after meeting old enemies, Ben has to transform into Alien X to save the universe from the Anihilaarg, a doomsday device created by the Contemelia to destroy universes . When Alien X transformed back into Ben, he gained a green and white jacket that had a hoodie, and a number 10 logo.
In Hot Stretch, Ben encounters Ester, a Kraaho, who stole a Nuclear Fusion Device. He meets Seebik, the leader of the Kraaho. Eventually, Ben develops a crush on Ester and together they put an end to Seebik's evil heist. Seebik is defeated and Ester becomes the new leader of the Kraaho.
In Of Predators and Prey: Part 1 Ben and Rook break up their partnership because of a fight and Ben's Plumber's badge is destroyed. Ben is then attacked by Khyber and his pet. He transforms into Crashhopper to battle, but Khyber's pet transforms into Mucilator and falls on Crashhopper, who transforms into Armodrillo and throws Mucilator.
Mucilator then transforms into Slamworm and goes underground, attacking Armodrillo. Armodrillo transforms into Heatblast and chases after Khyber, but meets a surprise attack by Crabdozer. Then Khyber introduces himself as the 'greatest huntsman in the galaxy', However Ben just mocks him. Heatblast tries to transform into Humungousaur, but transforms a new alien named Ball Weevil. At first Ben didn't know how to use Ball Weevil's powers, but then spits a ball and rolls around uncontrollably before seeing that the ball can explode. Crabdozer counters this by transforming into Terroranchula.
Ball Weevil flees, but Khyber defeats him by redirecting one of his attacks. The Omnitrix times out and Ball Weevil transforms back into Ben and falls down unconscious. Khyber then picks him up and starts gloating.
In Of Predators and Prey: Part 2, while being imprisoned in Khyber's Ship Ben eventually discovers from Khyber that Malware is also involved in the creation of the Nemetrix, the device that allows Khyber's pet to transform into predators of aliens, and that Dr.Psychobos using a corrupted blueprint of the Omnitrix retrieved by Malware, created the Nemetrix. Dr.Psychobos hired Khyber to collect Predator samples for the Nemetrix and they used Phil as a test subject. Rook then comes to Ben's rescue, revealing that their argument was part of their plan to lure Khyber and that Ben's Plumber badge was not destroyed. They manage to defeat Khyber and he crash lands. The wreckage of his ship is visited by Malware and Dr. Psychobos.
In Outbreak, the Plumber Headquarters is attacked by Dr. Psychobos who steals an Omnitrix component to perfect the Nemetrix. In the process, the now mutated Psyphon and his gang members create chaos until they are defeated by Ben, Rook and a squadron of Plumbers. Blukic and Driba manage to replace the component stolen and in this process they unlock new aliens. Ben also unlocks Kickin Hawk as a result of scanning Liam.
In Gone Fishin', Magister Patelliday is kidnapped by Captain Kork and his Mechaneer while he is fishing with Max, Ben and Rook. Max, Rook and Ben infiltrate Kork's headquarters and rescue Magister Patelliday as well as arresting Kork.
In Blukic and Driba Go to Mr. Smoothy's, Ben and Rook are busy chasing after Trumbipulor who is after 'Ultimate Power' which is revealed to be peanuts. Blukic and Driba are busy trying to go to Mr. Smoothy to buy a grasshopper smoothie. Ben and Rook manage to defeat Trumbipulor while Blukic and Driba manage to get smoothies. Ben also learns of the existence of a 23rd store of Mr. Smoothy.
In Malefactor, Khyber and his pet attack Ben at a festival. Ben recognizes Hypnotick's species and comes to a conclusion that this is just a distraction. Ben reaches the Proto-TRUK and finds Malware stealing data from it. Malware escapes and Ben shows a fear towards him in this episode.
In Arrested Development, Ben and Rook are fighting the Computron's Minions and meet Billy Billions. At first Ben mistakes him for a fan but then it is revealed that he is controlling the robots. As it turns out, Billy had a rivalry with Ben when they were young, though it was one sided. Amidst the rivalry, Billy fired a beam at Ben but since he was Diamondhead at that time, the beam was deflected and warped Billy to Dimension 12. Billy uses a De-Ager Ray on Ben and Rook, transforming them into young versions of themselves. Eventually, Billy accidentally causes an invasion of the robots. The robots are stopped by Ben and Rook who manage to revert to their original age. After that Billy is arrested and Ben once again shows Billy down.
In Bros in Space, Ben and Rook reach Revonnah, the home planet of Rook. Rook introduced Ben to his family and his crush. Later a Muroid attacks standing on two legs which is strange as they should walk in four legs. In the night, Ben finds out that there is a TV show about him. The next morning the Revonnahganders are harvesting and Ben tries to help them. At the end, it is revealed that Fistrick was manipulating the Muroids so that he can steal Amber Ogia, the sacred food, crop and fuel of the Revonnahganders. He is defeated with the combined efforts of Ben and the Revonnahganders.
In Ben Again, while Battling Eon, 11 year old Ben's mind gets switched with his 16 year old self. As 16 year old Ben, he finds the clues laid down by the 16 year old Ben who is inhabiting 11 year old Ben's body. 11 year old Ben manages to get his body back and defeats Eon. His mind gets switched with his 11 year old self. He lays clues for the 11 year old Ben inhabiting 16 year old Ben's body to find. Eventually, he manages to get his body back and defeat Eon.
In Showdown: Part 1, the Faction infiltrates Galvan Prime and they plan to humiliate and kill Azmuth. Azmuth teleports Ben and Rook to help him capture Zed and Dr. Psychobos. Khyber escapes with the Nemetrix while it is revealed that Malware was on Galvan B. At the end of the episode, Galvan B is destroyed with Malware being stronger than he was never before.
In Showdown: Part 2, Ben, Rook, Azmuth, Gwen, Kevin, Max, Blukic and Driba have a final showdown with Malware. Even Way Big is defeated by Malware. Ben then has a flashback of what happened when he was 11 and how he lost Feedback. He eventually regains Feedback by overcoming his trauma, and by absorbing the Helix's power, he defeats Malware once and for all.
In Vilgax Must Croak, Ben tries to escort Vilgax to Incarcecon, only for him to escape due to the Incurseans' intervention. In Store 23, Ben discovers a new dimension with its own version of him, whom he tutors in how to be a hero. In Special Delivery, Ben has to deliver goods for Baumann as a penance for wrecking his stuff. He quickly discovers that Psyphon is once again up to no good when he tries to steal a Dwarf Star. Ben manages to unlock Toepick, and defeats Psyphon with the new transformation.
In Rules of Engagement, Ben unintentionally breaks up with Julie, yet she helps him defeat Looma, with Ship's help. Ben starts going out with Ester. In T.G.I.S., Ben teams up with the Secret Saturdays to defeat Animo and V.V. Argost, developing a crush on Drew and becoming friends with Zak.
In Rad, Ben meets Rad Dudesman and teams up with him. Other episodes featuring his fight with the Incurseans culminate with Milleous's arrest and Attea's rise to power. In this arc, Ben also unlocks Astrodactyl and Bullfrag.
In Food Around the Corner, Ben helps a peace treaty to develop between the Lewodan and Appoplexian. In O Mother, Where Art Thou?, Ma Vreedle is searching for her son and threatens to destroy the sun, but Ben and his allies stop her. In Max's Monster, present-day Phil returns with a powerful transformation.
In Return to Forever the Forever Knights attempt to destroy Undertown. Mud Is Thicker Than Water introduces Ben's Lenopan cousin, Lucy, who helps uncover how Psyphon has been getting his hands on Plumber tech. OTTO Motives features Ben, Kevin, and Rook battling a robot named Otto.
The other episodes feature Ben's fight with Albedo, culminating with Albedo being turned into a 11-year-old version of Ben, Ben unlocking Atomix, and Zed being taken into Plumber custody after Khyber abandoned her.
In Something Zombozo This Way Comes, Ben must fight Zombozo, his clowns, and the Circus Freak Trio. Ben manages to defeat them, but not before into his fear of clowns returns. In Mystery, Incorporeal, Ben visits Gwen's college and defeats Michael Morningstar. As a reward for saving the day, Ben is granted an honorary degree, referring to himself as Dr. Tennyson, much to Gwen's chagrin. In Bengeance Is Mine, Ben fights Vilgax's Squid Monsters, who are wreaking havoc on the city. He defeats them with the help of an ordinary plumber named Bill Gacks.
In An American Benwolf in London, Ben is rejoined with Kai Green, his former crush. With her help, he defeats the Forever Knights before they can get Excalibur. In Animo Crackers, Dr. Animo's future self goes back in time to work with his present self. Chrono Spanner, a hero from the future, meets up with Ben and, together, they defeat both Animos.
In And Then There Were None and And Then There Was Ben, the episodes that celebrated the 199th and 200th episodes of the franchise, respectively, Ben teams up with his alternate timeline counterparts to take down Vilgax and the Evil Bens.
In Catfight, Ben went on a date with Ester. Eventually, Nyancy Chan intervened, but she was defeated and Ben resumed his date with Ester. In Collect This, Ben found out there's a show about him, run by Hokestar, Solid Plugg, Simian, and Deefus. Eventually, the Earth was sold to Collectimus, who, at the end of the episode, traded it for Ben's shirts. In The Vengers, Captain Nemesis, Kangaroo Kommando, Billy Billions, and Mazuma formed a team known as the Vengers. They try to replace Ben, but their true nature is eventually revealed to everyone.
In Cough It Up, Ben encountered Spanner again. Together, they defeated Psyphon, and the dehydrated Techadon Factory he was after was taken by Spanner. At the end of the episode, Ben revealed his suspicions regarding who he believes Spanner really is. In Blukic and Driba Go to Area 51, Ben learned how Blukic and Driba, reached Earth. Ben also managed to destroy B.L.R.R.T. and arrest Benevelon.
In No Honor Among Bros, Rook was affected by Fistrick's "bro essence" and participated in the Golden Fist Tournament. Although he won the tournament, he arrested the participants afterward, as it was an illegal tournament.
In Universe vs. Tennyson, Ben was dragged into a Celestialsapien court for recreating the Universe in So Long, and Thanks for All the Smoothies. Ben is eventually found not guilty thanks to Chadzmuth.
Other episodes featured Ben's fight with the Rooters while Kevin's true past is revealed. The battle culminated with the Rooters' defeat and their Plumber status being revoked by the Magistrata.
Clyde Five features Ben's cousin Clyde Fife and how upon obtaining the Cincotrix he becomes a hero. Rook Tales and The Final Countdown feature Rook's former sensei, Kundo, who turns into a cyborg at the end of Rook Tales and gets arrested at the end of The Final Countdown. The Ballad of Mr. Baumann features Mr. Baumann and Sheelane, who is Baumann's fiancee. Eventually, Ben helps Baumann to successfully reunite with Sheelane and Vulkanus is defeated. Breakpoint features Ben infiltrating Fistrick's gang who are committing crimes by impersonating as Ben. At the end Fistrick and his gang are arrested.
The Color of Monkey features Argit's new company and how Simian and Rojo cause trouble. They are eventually arrested. Vreedlemania features how the entire Vreedle family upon reuniting cause havoc in Bellwood until they are stopped by Ben. Fight at the Museum features Ben helping Kai to unsuccessfully protect the Orb of Pooma Poonkoo from Exo-Skull and Subdora who capture it for Maltruant. Ester also learns that Kai and Ben are meant to be 'together' in the future from Spanner who is confirmed to be not Jimmy.
From Hedorium to Eternity features 11 year old Ben who puts an end to Zs'Skayr's evil plan with the help of Jonesy, Gwen, Lucy, Cooper and Kevin. Stuck on You features Khyber enlisting the help of Skurd, a Slimebiote, to operate the Nemetrix. Eventually, the Nemetrix is taken back to custody with Khyber being arrested. Skurd now joins Ben as the Omnitrix because it has more DNA samples. In Secret of Dos Santos, Ben helps Kai to find the Temple of the Sky. Exo-Skull intervenes and Maltruant's history is revealed. Ben and Kai show feelings for each other with Kai even kissing Ben.
Malgax Attacks features how Vilgax and Albedo team up. Albedo uses Malware's remains to create the Malware Armor for Vilgax to wear so that he can defeat Ben. Albedo then attacks Azmuth, which ends up with Albedo's Ultimatrix being Disabled. Meanwhile, Ben is being defeated by Vilgax and he apologizes to Skurd (He had him taken out of his Omnitrix by Azmuth because Skurd was annoying) and the two team up again to defeat Vilgax. Vilgax is eventually killed by his ship's core meltdown. Also Malware's fate is unknown as the armor oozes out of Vilgax's petrified body. Hence, it could be that Malware is still alive.
Charm School and Third Time's a Charm finish the trilogy that was started by Charmed, I'm Sure. In the trilogy, Charmcaster has turned Adwaita and Darkstar into stone totems and plans to become the most powerful sorceress of all time. She even manages to turn Gwen, Hex, and Bezel into totems until she is cleverly beaten by Gwen and is now trapped in her own bag. Gwen acquires the Charms of Bezel and now thinks that she and Charmcaster can become friends. Adwaita gets away and Darkstar is arrested. In The Most Dangerous Game Show, Charles Zenith hosts a show which would decide who would marry Ben. Kai wins the contest and all the girls who lost are rescued from the Null Void . Charles is arrested, Ben and Ester break up on good terms and Ben and Kai become a couple.
It's a Mad, Mad, Mad Ben World: Part 1, It's a Mad, Mad, Mad Ben World: Part 2 , Fight at the Museum, Let's Do the Time War Again, Secret of Dos Santos, The End of an Era, and A New Dawn feature the Time War. In the Time War, Maltruant puts himself back together and orders Exo Skull and Subdora to find his missing parts. After becoming whole again, he orders Eon, Exo Skull and Subdora to get some Time Beast eggs for him. Even though Ben, Rook, Ben 10,000 and Paradox intervene Eon manages to get two Time Beast eggs for Maltruant.
After this Maltruant goes to the Future and steals the Dwarf Star and the Anihilaarg and fuses them to create his modified Anihilaarg. Future Ben, Gwen, Kai and Spanner who reveals himself to be Ken, Ben's son fail to stop him. But then Spanner brings past Ben and Rook to help. However Eon arrives with a chariot pulled by a Time Beast. After Eon is betrayed, Maltruant escapes to the time-stream with Ben and Rook following with the help of their Time Cycles. They eventually crash to the past where Ben meets George Washington and battles young Vilgax.
Then Ben and Rook continue their chase which leads them to a Contemelia ship. The Contemlia reveal that they create Universes, they do not destroy them. Maltruant activates his modified Anihilaarg to create the Universe in his own image however the energy of the Anihilaarg is absorbed by Feedback who redirects it to Maltruant dividing him into many parts. Paradox then comes revealing that Maltruant is trapped in a time loop in which he is doomed to lose. Ben and Rook than witness the creation of the Universe after parting with Skurd who joins his ancestors to seed life across the universe. At the end of this series, Ben calls Gwen and decides that he, she, Rook and Kevin are going for a road trip across the entire Universe.