Season 2

After the battle with Vilgax, Grandpa Max retells his story to Ben about his past. He was with an organization that was not known to exist, referred to as "The Plumbers," a group of people who track down extraterrestrial life. Meanwhile, they meet Phil, an old partner of Grandpa Max. But they soon find out that he steals a device, called the Null Void Projector, to selfishly use it to make money by appearing to capture aliens that he alone released himself.

At Yellowstone Park, Ben and Gwen inadvertently discover a new form on the Omnitrix: Cannon Bolt, an armadillo-like alien that Ben isn't too fond of. Soon after, a meteor comes crashing down to the park, containing a planet-devouring, tick-like alien. On top of that, three other aliens arrive with it, and worship it as their savior, the "Great One." Powerless to stop the planet-eater with his regular forms, Ben must rely on a new form he knows nothing about.

At a city, Ben, Gwen, and Grandpa Max are waiting outside a video game store to purchase the newly-released Sumo Slammer video game. Gwen and Grandpa Max go the book store, but when they return to check on him, Four Arms comes out of the store by force. They return to the RV, and find that Ben is already there. Gwen yells at Ben for what he's done, but he has no clue of what she's talking about. But as she gives direct evidence that Four Arms was attacking the city, Ben heads out to find the perpetrator, using the identity of his aliens to ruin his current reputation as a hero.

In this "how 'bout?" episode, Gwen gets the Omnitrix and the power that comes with it.

In the middle of nowhere, Ben, as Diamond Head, fights Kevin 11, who is still in his mutated form. As they fight, they are taken to a ship, where a battle between different aliens are held. But when a mechanical droid named Slix decides to create a bond with Ben and Kevin as a team, they immediately turn his idea down. But with no choice, they must find a way out. Will Ben and Kevin learn the importance of teamwork?

At a museum, Ben sits and reads a comic, daydreaming about himself as a super hero. As Gwen interrupts him, she is not happy how Ben treats the artwork. His day has been a bore, but when an alien vessel arrives, an alien named Volcanus and the bounty hunter Sixsix come to pursue the Biocenthium alloy to complete a mixture with Element X to create a bomb, strong enough to destroy a whole solar system. Suddenly, Ben meets The Galactic Enforcers, a group of three who serve in protecting the galaxy under the conduct code. Ben is intrigued by their heroic appearance, but are they really something to be looking up to?

When Ben and Gwen argue over a birthday party to occur in the next few months, Grandpa Max is distracted by their quarreling and almost hits a young boy camper. To ensure the boy's life, they head to Camp Opinicon, only to find no people around. As they investigate the premises, they find twins, whom were also hiding from something that may have a connection to the lifeless camp. Grandpa Max readies to leave the area with the children, only to find that the RV's engine is clogged with a mysterious fungus. While the kids take in shelter in a nearby cabin, Grandpa Max is captured. Now Ben must come to the rescue to discover a new alien form, as well as a way to destroy the evil alien Myceloid Monsters and their Fungal Master, and learn the benefits of what sharing can do.

In Texas, a group of men discover a mysterious mask belonging to Ah Puch, the Mayan god of death and destruction. The mask is the key to the ultimate weapon in the world, known as the Sword of Ekchuah. However, when Grandpa Max and his grandkids learn that the mask is discovered, he impatiently sets out to obtain the mask, so that it does not fall in the wrong hands. Unfortunately, they find out that Enoch of The Organization is after it as well. The kids worry of how Grandpa Max has become, but with Enoch in the way, will Grandpa Max find the sword before him?

Hex's niece, Charmcaster, enters the underground prison he's held at to release him out of his cell. With her help, Hex was able to regain most of his powers after being given his magical staff. Meanwhile, Ben, Gwen, and Grandpa Max head to a magic convention held in Las Vegas, and in there, Gwen finds the legendary Keystone of Bazell. With it, she gains the powers of Lucky Girl once again, but will it last after finding out that Hex and his niece are after it?

Our heroes ride a jet belonging to Grandpa Max's old Friend, Donovan Grand Smith, who owns an underwater resort. At the entrance, they receive a warm welcome from Donovan himself, though they also meet with his grandson, Edwin, who didn't seem to be excited about their guests. Later, when Edwin, Ben, and Gwen enter the Undersea Manta Ray, a giant submarine, they encounter strange aliens that threatened to destroy the whole resort. While the kids find a way to cooperate with each other to find the source that lures them in, Donovan himself learns a few lessons in how to bond better with his grandson.

A terrorizing nightmare of Ghostfreak is half the trouble for an unnerved Ben, as a tour of an important academy that Gwen wishes to attend is disturbed by the uncanny alien's manifestations and the antics of Acid Breath, Frightwig, and Thumbskull.

The Tennysons arrive at a swamp, where a festivities of Gatorfest start first thing the next day. Gwen finds Ben playing around with the Omnitrix, and she warns him that it may create unusual problems. Without heeding Max and Gwen's warning, he pops the face out, and the Omnitrix acts up. Right away, something was wrong, though it was gone unnoticed, at least, until the next day. Gator-fest was going along well, but the giant frog of Dr. Animo comes in to disrupt it. Dr. Animo has returned, and he wants to take revenge on Ben. But when Ben goes alien, he transforms into a hybrid alien with unbalanced attributes. Will Ben ever learn his lesson in listening for a change?

The Megacruiser flies solo in space, and inside Kevin examines the giant ice block found in space. Inside the mass, held Vilgax, and Kevin underestimated his current situation. He was very much alive and well, and they soon create a partnership after learning that they were both after the same person. On Earth, Ben plays around with the Omnitrix, hoping to find a better way of controlling it. Eventually, he finds the master control of the Omnitrix, giving him the ability to alternate between aliens, as well as prolong his duration with a form. Although his discovery has given him a stronger advantage, will it be enough to stop the danger that lies ahead?