Ben's secret identity is revealed to the entire world, and he is now a megastar superhero loved and favored all over by kids, teenagers,and few adults, but distrusted by many adults. After having a long talk with Julie in Ben's brand new car, Kevin and Gwen arrive in Kevin's car and tell Ben where to find the one who told his secret to the world and they go to "pay him a visit". When they arrive they find out how the tattletale, a young boy named Jimmy Jones, figured out Ben's identity and with his help discover an alien attack in Florida. When they arrive at the site (using Kevin's new jet), Ben is arrested by the local police. Luckily, NASA needs the assistance of the Plumbers so Gwen and Kevin manage to get Ben out of jail. After being briefed on the situation they try and fail to foil the a robbery by an unknown alien whose DNA is scanned by the Ultimatrix. They follow the thief to find out that he is an alien refugee named Bivalvan from the Andromeda Galaxy who was only stealing the NASA equipment to build a ship he could use to go home. However, this would require detonating a nuclear bomb, which would destroy central Florida. Ben manages to stop him by wrapping him in Ultimate Spidermonkey's web. Bivalvan informs them that an alien named Aggregor is after him and some other aliens that were kidnapped, but they leave him in the web and say that the Plumbers will take him home safely. Later, Ben reluctantly returns to school with some encouragement and a first kiss from Julie. He goes in and is soon greeted with applause, particularly from his old bullies Cash and JT. Some time later Bivalvan is found and subdued by Aggregor.

Ben needs to be at more than one place at once; he has to fight the Forever Knights with Kevin, go to Julie's tennis game, and see a Sumo Slammers movie. So Ben transforms into Echo Echo and divides in three and changes back to Ben, but this time there are three Bens with one part of his personality. One is the real Ben, the other is the honest, intimate Ben, and the last one is the immature Ben. The Honest Ben goes with Kevin to the museum, the Immature Ben stays to watch Julie's match, and the real Ben goes to see Sumo Slammers. Urien (a king of a fraction of Forever Knights) is after some strong suit of battle armor. When Honest Ben and Kevin are in danger, Urian is in the battle armor and attack Intimate Ben and Kevin, the real Ben and the immature Ben have to help them stop Urian. All the Bens go Echo Echo and change back into one. Ben later defeats Urian with Lodestar and heads to back to the tennis match, where its revealed that his plan backfired and he is scolded by his friends for his foolish plan which ruins Julie's game (although she won) and causes Julie to angrily storm off. Gwen angrily storms off too, along with Kevin, leaving Ben all alone to repent for what he's done.

After Jimmy Jones reveals Ben's identity, some of his enemies (such as Zombozo, Rojo, Charmcaster, Vulkanus, and Sevenseven) team up to try to attack his family. Now Ben and his friends have to protect them no matter what.

After defeating Ssserpent with Fourarms, Ben's celebrity status lands him in a starring role in a video game. The developers ask him to show off all his aliens' different moves so they can be implemented into the game. In reality, TV reporter Will Harangue has been using the video game to build a giant spider-like robot that knows all of Ben's aliens' moves from when he openly showed them. After being defeated twice by Harangue's robot, he challenges Ben to a final showdown on live TV. After realizing how Harangue's robot can predict his aliens' moves, Ben uses Humongousaur with sumo slammer moves to fight it. He damages it until it has lost control, but its still shooting randomly. Ben then turns into Nanomech which was the only alien with moves that were not installed into the robot, Ben is able to defeat it from the inside.

In the Himalayas, Dr. Animo and his mind-controlled Yeti were fighting with Ben. Ben, as Brainstorm, mind-controls the Yeti and frees him. Kevin and Gwen deactivates the Devalution bomb. Gwen calls the Plumbers to take them, the Plumbers informed them that there is an alien action in Bellwood. Ben encounters the turtle-like alien Galapagus, who was on a rampage to find Ben. He escaped from Aggregor and tells Ben how he ended up captured alongside four other aliens in a plot to permanently absorb their powers.

Eager to escape his containment suit, P'andor (one of the aliens who were captured by Aggregor) offers a huge cash reward to anyone who can break him out of it. Everyone who tries to break the suit ranging from Buzz, Hammer, and Surgeon fails, save for Kevin, who uses a piece of Taednite to pierce it. But, when Kevin's Plumber's badge senses that the contents of P'andor's suit are radioactive, he stops trying to open it. Enraged, P'andor then offers Buzz, Hammer, and Surgeon an even bigger reward if they capture Kevin.

When Ben, Kevin, and Gwen investigate an odd string of thefts by the Forever Knights, they learn that Argit is using Andreas (one of the aliens being hunted by Aggregor) to frighten them into making him their leader. Argit's plans go bad when the Forever Knights eventually revolt, and throw him into a dungeon with Ben and the others. When they discover that the Knights plan to execute Andreas, they break out and save him. But when a Forever Knight sets a bomb that would level the entire castle, Andreas sacrifices himself to absorb the force of the explosion. Although Ben and company believed him to be dead, Andreas survived the explosion. Unfortunately, the endeavor of stopping the bomb made him too weak to resist Aggregor as he recaptures him.

After ambushing Ben at his house, Ra'ad (one of the aliens captured by Aggregor) blames him for letting Aggregor recapture the other four aliens through the Ultimatrix. While trying to resist being scanned by the Ultimatrix with his electric powers, Ra'ad causes it to malfunction, and ends up deactivating it while both his and Ben consciousnesses trapped within his body. Despite Ra'ad's protests, Gwen and Kevin reactivate the Ultimatrix, and separate Ben from the alien. But in doing so, they alert Aggregor to their location. Ra'ad flees, leaving the others to be wiped out by the Osmosian. After Kevin scolds Ra'ad for his cowardice, the alien decides to sacrifice himself to save Ben, and is recaptured by Aggregor in the process. After the battle, Ben swears that he will do whatever it takes to save the captured aliens.

Ben meets his favorite superhero idol Captain Nemesis when he shows up to save actress Jennifer Nocturne, however Captain Nemesis is displeased when Ben gets kissed by the actress instead of him. Captain Nemesis' assistant, Simons meets up with Will Harangue about staging an event that will put Captain Nemesis back on the front page of each magazine. When Ben wins, The Captain goes to extreme lengths to prove everyone that he is the best superhero of all time. He captures Julie and Jennifer and Ben tries to call Julie to go to Mr. Smoothy's he gets a message from Captain Nemesis telling Ben to try and save her. Ben goes to rescue Julie and Jennifer by going ultimate Humongosaur and uses goop to rescue Julie. Kevin and Gwen rescue Jennifer and Jennifer loves Kevin. Ben defeats Captain Nemesis with Water Hazard and Captain Nemesis gets arrested. But when Jennifer falls in love with Kevin, Gwen threatens her to get her away from Kevin.

With all five aliens in his possession, Aggregor tries to return home to absorb their powers. A Plumber ambush damages his ship, so he instead heads for Los Soledad, in order to use Prof. Paradox's time machine as an alternate power source. Despite Ben, Kevin, Gwen, and Grandpa Max's best efforts, Aggregor succeeds in absorbing the aliens' forms and powers, turning himself into an unstoppable amalgam of the five.

With his new powers, Aggregor easily defeats Ben and his friends. Azmuth tells Ben that Aggregor intends to steal the Map of Infinity, a complete map of the entire universe. With it, he'll be able to find the Forge of Creation, the birthplace of the universe. He further explains that Aggregor stole the five aliens' powers to protect him from the traps guarding the map, which is split into four pieces. In order to keep him from assembling the map, the team tries to take one of the pieces first. Aggregor, however, simply follows them and steals it after they disable the traps for him.

After "helping" Ben, Gwen, and Kevin stop the Forever Knights, Cash and JT start a TV show with Oliver as their cameraman. Ben, Gwen, and Kevin play along for awhile. Upon tracking the Forever Knight, Ben, Gwen, and Kevin learn what the Power Decoupler is being used by the Forever Knights and attacks them with some interference from Cash and JT. Afterwards, Psyphon shows up to attack Cash and JT after seeing the broadcast of them taking the credit for given Ben his battle tactics. After Psyphon explains he tapped into Vilgax's power, he begins to defeat Ben. He is just about to defeat Ultimate Spidermonkey when Cash and JT fire the weapon the Forever Knights were charging, and it absorbs Psyphon's power. Ben light knocks him with his fist and Psyphon falls to the ground. Cash and JT are ecstatic, but find no-one saw them do it, and the weapon drained the camera's battery as well, leaving them with no recognition, and Cash shouting after Ben and the others.

Ben, Gwen, and Kevin travel to the center of a water planet, namely Pisces, Ripjaws' home planet in an attempt to find Aggregor. They end up getting help from Magister Pyke, one of Ripjaws' species. The planet has a 2% solid core, which holds an instrument that holds the planet's water together in a gravitational pull. Aggregor takes the instrument and reveals it to be a piece of The Map of Infinity. As the planet is pulling apart, Aggregor escapes. Ben transforms into Goop and uses Goop's anti-gravitational UFO in an attempt to fix the centripetal force holding the planet together. Goop vanishes, and Kevin says he was atomized and spread throughout the ocean. The water then turns green, and Goop pulls the planet back together.

Gwen, Ben, and Kevin follow Aggregor into a mystical dimension called Legerdomain with the help of Charmcaster, who was born there. They believe Aggregor's target to be the Alpha Rune worn around Addwaitya's neck, which they suspect is a disguised piece of the Map of Infinity. Gwen and Charmcaster work together several times, and the two develop a bond that seems to lead to Charmcaster changing her ways. While the group tries to steal the Alpha Rune, Aggregor uses the distraction to knock Addwaitya out and take it himself. Gwen, Ben, and Kevin escape Legerdomain with Charmcaster's help, but Charmcaster remains behind to free Legerdomain from Addwaitya's rule. Ben promises Gwen that they'll find a way to return and help Charmcaster after Aggregor is defeated.

With the fourth piece of the Map of Infinity almost in Aggregor's clutches, the gang chase him through the artificial planetoid known as Perplexahedron.

Azmuth is upset with Ben, Gwen, and Kevin for letting Aggregor get all the pieces of the Map of Infinity. Ben resolves to become Alien X to get Bellicus and Serena to cooperate. When this fails, Paradox arrives and changes Alien X back to Ben. After a brief argument, Paradox and Azmuth explain that the Forge of Creation is where all Celestialsapiens (Alien X's race) are born, and Aggregor hopes to absorb the powers of a newborn Celestialsapien and become all-powerful. Paradox takes them to the Forge of Creation, where an accident pulls Ben's ten-year-old self out of the timestream.

With Kevin having absorbed Ben's aliens and become insane once again, Ben and Gwen have to go to the null void prison in an attempt to stop Kevin from destroying all the people there. We learn more about how Kevin got his material absorbing powers. In the end Ben thinks Kevin should be put down.

When Argit and the Vreedle Brothers team up, they come up with a plan to attack the Plumber Academy.

When Ben and Gwen are faced with an unexpected enemy, Gwen turns to Darkstar for help.

Ben and Gwen are forced to go to Darkstar for help when they come across their most deadly, most unexpected foe yet.