Season 3

When Gwen is abducted, Ben as XLR8 follows her abductor to the future where they discovered that her abductor is the future Gwen and they discover his future version of Ben and Grandpa Max. In the future, Dr. Animo revives Vilgax and plots to open the Null Void chamber. Both Bens must work together to stop them.

When Ben is hypnotized, he begins breaking the law while sleepwalking. Once the evil hypnotist called Sublimino discovers the aliens at his disposal, he plots to put hundreds of people under his control forever.

Dressed as Pilgrims, to honor their history, while in the streets of Salem, MA, Ben, Gwen, and Grandpa Max witness an explosion of a nearby building. But when Ben rushes to the rescue, Charmcaster is there waiting with a spell to take over Ben's body and the Omnitrix. Only things go awry and Gwen and Charmcaster switch bodies. Gwen goes to prison and the sorceress is brewing a plan to gain the Omnitrix. Now Gwen must find the way to get out of prison, alert her family against Charmcaster, and get her own body back using every trick up her sleeve... or Charmcaster's.

Ben, Grandpa Max, and Gwen come upon a bizarre Christmas theme park run by an evil entity who thinks Grandpa Max is Santa Claus and proceeds to trap him.

Ben, as Wildvine, is fighting against an evil werewolf and is bitten. The Omnitrix times out and Ben turns back to his human form. Then, when the werewolf hits the Omnitrix, it starts to mess up and act weird. After all of this, Ben starts to get a crush on a girl that he meets. But things change, as Ben slowly starts to turn into a werewolf himself.

The Tennysons stay in as it rains outside, and Ben plays a video game to pass the time by. When Gwen decides to join in, Ben is jealous of how she's a far superior player. Instead, Ben decides to transform to Upgrade, and merges with the game console. Gwen makes an attempt at shaking him off, but suddenly, a lightning strike causes them to transfer into the video game itself. The only way Ben can use the Omnitrix is to find coins with the different aliens on it. To get out, they must find the Upgrade coin before an evil being uses it to escape into the real world.

Ben's alien heroes are starring in a silly network cartoon called Super Alien Hero Buddy Adventures and his favorite action hero Kangaroo Commando has been pulled off the air by the same network, so Ben tries to get him back on television and get credit for the alien heroes.

In order for Ben and Gwen to learn the value of hard work, Grandpa Max takes them to a farm. Meanwhile, an alien mummy arrives to uncover a rare and dangerous element.

While attending the Little League World Series to see his home team play, Ben discovers that the opponents are actually robots posing as kids. They also have plans to replace the President with one, as well.

Grandpa Max takes the kids to Chicago to see one of his favorite band, Shag Carpeting. The kids meet a weather reporter who forecasts the weather with a robot named S.A.M. He uses the robot to create rain, but a giant creature forms! Ben quickly takes care of it. The reporter tries to destroy S.A.M., but he convinces him not to. S.A.M. then goes into the sky and begins to cause chaos. The reporter tries to stop it again, but he is no longer in control. Can Ben destroy the robot and save a city from disaster?

While driving on a Florida highway, a bus of escaped felons rams into the RV. Ben transforms into Stinkfly (though not intentionally) and tries to stop them. With a little help from Grandpa's handy driving, and a magic spell from Gwen, the felons are put back in jail. On the news, the Tennyson's hear about purple lightning delaying a space shuttle launch. Remembering the lightning from the encounter with the werewolf and mummy aliens, they head to Cape Canaveral. At the Space Center, Ben comes under attack by the werewolf and mummy aliens, and new Frankenstein alien. However, why is the purple lightning occurring, and what ties does it have to an old "friend"?

Ghostfreak's return spells disaster for our heroes. Grandpa Max and Gwen must deal with the mummy alien in space while Ben deals with Ghostfreak and Dr. Vicktor on Earth. Ghostfreak then reveals his master plan: he plans to blanket the Earth with Coronium so that sunlight will not reach the planet so that he may rule. With the power of a new alien in the watch, can Ben stop Ghostfreak, and save Grandpa and Gwen?

While snowmobiling, two guys accidentally release an alien named Xylene from a strange container. At a park, Ben (as Wildmutt) steals Gwen's kite, so she casts a spell to make dogs attracted to him. Grandpa Max seems sad to be in St. Louis since it is where he met his wife. Xylene attacks, and Grandpa Max comes to defend, only to recognize her. Xylene reveals that she came to find the Omnitrix since she lost it when Vilgax attacked her ship. While Grandpa Max and Xylene talk about the past, a robot emerges from the area where Xylene was and attacks Ben and Gwen. The mechadroid attacks twice, taking Grandpa Max with him. Now Ben must work with Xylene (to his dismay) to save Grandpa Max.