Season 3

Vilgax, after conquering 10 planets, comes to Earth to destroy Ben.

Ben, Gwen and Kevin race to collect the Omnitrix's missing forms and make it to the battle with Vilgax on time. Meanwhile, Kevin discovers that his new transformation has some benefits.

Ben, Gwen and Kevin discover that Vulkanus is planning to drill the center of the Earth and drop a bomb into the hole. Destroying the planet.

A species of goat-like aliens comes to Earth for a popcorn festival. Ben, Gwen, and Kevin have a big problem when one of the aliens eats meat and turns into a monster.

An alien named Probity seeks help from Ben to stop the on-going war on her home planet.

Ship's owner decides he wants him back and hires some repo men to retrieve him. Ben and Kevin go to court to take care of things legally, leaving Gwen and Julie to face the repo men.

A bounty hunter tries to remove the Omnitrix from Ben.

A series of earthquakes awakens a HighBreed officer who has been hibernating deep under the earth’s surface. He believes the HighBreed have lost the war and activates a fail safe device that is programmed to destroy. Ben must now work together with Gwen and Kevin not only to save Grandpa Max, but also the world from this "giant" problem.

Kevin is beginning to lose all hope that he will someday return to his human self. He then meets a girl who doesn't seem to mind the form he is in. Kevin finds himself under her spell, quite literally, as Charmcaster has come back to exact revenge on Ben and Gwen. Kevin, under Charmcaster's spell, has no choice but to obey his master and destroy Ben and Gwen.

Vilgax promises Ghostfreak to spring him out of prison as long as he tells him the secrets of the Omnitrix, but when Ghostfreak betrays him and turns his people into his minions, Vilgax comes to Earth and asks for Ben, Gwen and Kevin's help to get rid of Ghostfreak.

Kevin makes a temporary truce with Darkstar to retrieve an artifact that will return them into their former selves.

Ben, Kevin and Gwen come across an alien box that can forms into a robotic version of whatever it sees. It power becomes a liability when the Vreedle brothers decide to take the box for themselves.

Zaw-Veenull asks Ben to deliver Prince Tiffin to Jarret in order to keep peace between the two species. Shortly, after their trip in space, the Omnitrix malfunctions and turns Ben into an Appoplexian named Rath who wants to fight anything that breathes.

The Omnitrix transports Ben, Gwen, and Kevin to a planet called Primus, which turns out to have been created by Azmuth. They must stop Vilgax from stopping the Omnitrix at its source.

Despite being warned by Paradox, Gwen travels back in time to prevent the accident that turned Kevin into a monster from ever happening. Gwen returns to the present only to find that her time traveling caused a series of events that led to Hex ruling the world.

While sick, Ben is visited by old friend Tetrax, who demands that Ben hand over Chromastone.

The Plumber's Helpers are called upon by Grandpa Max to rescue him from an abandoned space station where he's being attacked by Ben! The team must now find a way to work together as they try to save Max, stop Ben, and keep the space station from crashing to Earth.

Kevin returns home to find his house ransacked, so he enlists Ben and Gwen's help to find out who did it and why. They soon cross paths with Ragnarok, a deadly criminal who recently broke free from the Null Void and is in search of a special key. Kevin is intent on stopping Ragnarok from obtaining the special key, especially after he learns the truth about Ragnarok and his father.

Albedo has stolen the Ultimatrix from Azmuth and has used it to kidnap Gwen and Kevin. Ben goes to face Albedo and rescue his friends when he quickly discovers that Albedo has been working in conjunction with Vilgax. Ben is defeated by the pair and gives up the Omnitrix to save himself and his friends.

Powerless, Ben goes aboard Vilgax's ship and faces off with Vilgax to stop his invasion of Earth in their final battle. Albedo gives Ben the Ultimatrix and Ben gets his old aliens and their evolved forms.