Taking place shortly after the events of the original Ben 10, Ben, Gwen and Grandpa Max spend their evenings fighting aliens on the streets of Bellwood. During a battle against a robotic tank, Ben as Upgrade and Gwen argue about the best way to defeat it, leading to Gwen using a magenta/pink-colored dismantling spell on the tank while Ben is attached to it. Unknown to the children, this leads to a malfunction in the Omnitrix.
Later, after a mishap in school where the Omnitrix accidentally teleports his homework, Ben is grounded by his parents and forced to stay home and do a history report. Ben attempts to work on the report before the Omnitrix teleports his laptop away as well. Shortly afterwards, Tetrax Shard arrives and tells Ben that Azmuth has asked to meet with him. They go to meet Azmuth but are attacked by an evil version of Waybig. Tetrax and Ben fight the alien, who is also teleported into the Omnitrix, though neither of them is aware of it. Tetrax decides to take Ben to search for Azmuth and activates a new function on the Omnitrix. Before he can explain this new ability, the ship is attacked and Ben is sucked out into the atmosphere, falling to the ground as Diamondhead. It is later revealed that the new ability prevents Ben from returning to human form when he times out, simply switching alien forms. Ben as Fourarms arrives at Stonehenge and is attacked by a weaponizing Galvanic Mechamorph who demands to know about the alien that attacked Ben. Ben tries to explain he knows nothing, but the Mechamorph only continues to attack and the Mechamorph’s teleporting ability causes the pair to carry their battle across the globe, destroying part of Stonehenge and nearly damaging Cristo Redentor in Rio de Janeiro and fighting at the Great Pyramids in Egypt before arriving back in Bellwood. Ben transforms into Grey Matter and manages to escape the Mechamorph.
Meanwhile, Gwen and Grandpa Max receive a call from Ben’s parents Carl and Sandra informing them that Ben has escaped the house. They go in search of him, only to find Tetrax and discover Azmuth’s ship. Looking at the ship’s log, they discover that Azmuth disguised it as a semi truck to track down and fix the malfunctioning Omnitrix, but crashed and was destroyed by the evil Waybig. After escaping the Mechamorph, they soon encounter Ben back at his house and Tetrax restores Ben’s Omnitrix to normal just as the Mechamorph catches up to them. Gwen sees how the Omnitrix reacts after Ben returns to human form and deduces what has happened just as she, Ben, Tetrax and the Mechamorph are transported into the Omnitrix itself.
Inside, Ben and the Mechamorph continue to battle before being attacked by a swarm of Stinkflies just as Gwen and Tetrax are ambushed by a herd of Wildmutt. The four catch up with each other and they realize that the evil Waybig is inside with them just as he resurfaces. The Mechamorph, who is revealed to be Azmuth’s father, attacks the Waybig in revenge for killing his son while Gwen explains to Ben about the malfunction that she caused to the Omnitrix when she cast the dismantling spell on the robotic tank while Ben was attached to it. She uses Azmuth’s father to reverse the transportation and return them to Earth. Unfortunately, the Omnitrix malfunctions again and transforms Ben’s parents into Wildmutt and Heatblast, causing Gwen to realize that the evil Waybig is Azmuth himself. Leaving Grandpa Max and Tetrax to handle his parents, Ben and Gwen follow Azmuth’s father and Azmuth to the city park where Ben transforms into Waybig to subdue Azmuth and hold off his father while he and Gwen try to reverse the transformation. Between the two Waybigs, they do a few hundred million dollars in property damage from smashing huge building after huge building (there are most likely no one in the buildings as the battle takes place in the morning before people arrive to work in them, which may be why they are not concerned about huge loss of life). They soon convince Azmuth’s father that his son is the very alien that they are fighting and the three work together to convince Azmuth to regain control of himself, use his father’s Mechamorph abilities to fix the Omnitrix and return Azmuth to normal. Azmuth reprimands Ben and Gwen for their errors and reveals his father is a Grey Matter wielding a Mechamorph-type armor.
Returning to Ben’s house, Azmuth restores Ben’s parents to normal and repairs the Rust bucket, previously destroyed in the battle, before leaving to reconcile with his own father. Ben’s parents, having forgotten that they grounded Ben, tell him to enjoy his fishing trip with Grandpa Max and Gwen. Ben declines, having learned to be more responsible, and stays home to finish his history report for school. The movie ends with Ben, Gwen, and Grandpa Max on another road trip where they encounter Doctor Animo and the three prepare for another exciting battle.