Professor Paradox informs the team that Vilgax has successfully taken over Earth

The story starts as Vilgax invades Bellwood with a gigantic Null Void Projector, releasing hundreds of Null Void prisoners into the city.

Ben10 attempts to transform into Aliens, but Professor Paradox stops him, stating that now is not the right time to use Alien X.

Instead, they split up to tackle the invasion.

Ben Aliens Protector Earth fights his way to Psyphon (who's coordinating the attack from ground level), but when Ben defeats Psyphon, he brings to life a Mr. Smoothy sign as a distraction.

He defeats Mr. Smoothy by quickly hitting it with every alien in his arsenal, except for Cannonbolt and Aliens X, and in the process puts the Omnitrix into reboot mode and locks out most of his arsenal.

Azmuth appears on he shoulder and examines the Omnitrix, saying that it needs to recharge before he can access all aliens again.

To make matters worse, Professor Paradox informs the team that Vilgax has successfully taken over Earth, so he sends them back far enough in time to destroy every power source for his Null Void Projector possible in the whole galaxy,

stating that the first is being recycled from the toxic radioactive waste of Vulpin: Wildmutt's home planet, however only Spidermonkey, Big Chill, Humungousaur, Swampfire, and Cannonbolt are available.

(Only Swampfire and Goop are available in the DS version).

Arriving on Vulpin, Ben's orders Gwen, Kevin, and Ship to stay put, because if Vilgax arrives, it will take all of them combined to hold him off.

He fights his way throughout the refinery, going through Vilgax's bioids, the local Vulpimancer, and a giant two-headed snake.

BenX then finds the Vreedle Brothers (Darkstar replaces the Vreedle Brothers in the DS version) and manages to defeat them.

Then, Ben finds a holographic message from Max, stating that the one Ben destroyed isn't the only one, and responds that he's currently on his way to Terradino: Humungousaur's home planet, to destroy the energy core there.

Goop is then unlocked. (Humungousaur and Spidermonkey are unlocked in the DS version).

Arriving on Terradino, they find another message from Max, stating that the energy core is located in the nearby temple and that Vilgax's forces are all ready there.

He once again orders his companions to stay and hold off Vilgax if he shows up.