Ben Tennyson, Ryan Kelley, Gwen Tennyson, Galadriel Stineman, and Kevin Levin, Nathan Keyes, negotiate with a group of black market dealers attempting to sell alien nanochips that are interfering with the Omnitrix. One of them reveals herself to be Elena Validus, Alyssa Diaz, Ben and Gwen's childhood friend. Elena explains that she had set up the negotiations to lure Ben into helping locate her abducted scientist father.
As Ben agrees to help her, the chips spring to life and attack, controlled by a man on a catwalk. The group fights them, and in the process the suspicious man and the dealers escape. While Elena claims she is not responsible for the attack, Kevin and Gwen are suspicious of her.
At their headquarters, the trio, along with Grandpa Max Tennyson, Barry Corbin, study one of the chips salvaged from the fight, learning that they are a hybrid of organic and technological components. Elena breaks in and Max orders her to leave, explaining that Elena's father Victor Validus was his apprentice, who was dishonorably discharged after stealing the original chips. Ben refuses to believe that Elena is like her father, and breaks ranks with Max and teammates to help her.
While Max is away, Gwen and Kevin investigate Victor and discover a video of Max interrogating Victor, in which Victor insists that
> "The Hive," the mind intelligence behind the chips, is coming to take over the planet as they are revealed to be able to possess people.
Meanwhile, Ben and Elena arrive at Victor's old laboratory which had been cleared by the Hive, where they find evidence that Victor was studying and upgrading the chips. Elena reveals that her father had become erratic before disappearing, and had stopped returning home. He also appears to be the man from the rafters controlling the chips. A mob under the control of the chips ambush Ben and Elena, forcing them to retreat. The Omnitrix again experiences interference around the chips and keeps Ben from transforming, but Ben utilizes a scanning function to temporarily repel the mob and allow him and Elena to escape. They head to the Ship-It building to investigate further, though Ben is somewhat suspicious of Elena himself, realizing the mob expected him and Elena to head towards the lab and set a trap for them.
Ben finds an order slip made out for that day when Elena claimed that Victor had already been missing for weeks. Having reached the building, Gwen and Kevin are too late to stop the distribution of the chips. Instead, they are met by one of the Ship-It employees, who is also under the chips' control. He summons another larger chip swarm, now capable of forming solid, weaponizable shapes, to attack Gwen and Kevin, damaging Kevin's car during a lengthy chase.
Upon joining them, Ben uses Humongousaur, Dee Bradley Baker, to defeat the swarm, destroying Kevin's car in the process. By the time they return to headquarters, the chips have spread across the globe and number in millions. Gwen realizes the swarm's new ability is a sign that they can adapt to threats and become smarter. The group also deduces the chips have a queen, as the chip's hosts have mentioned her. They believed that they can stop the chips by destroying her, but during their search, Max is possessed.
Pulling together, the group notice that while world population centers are all infected, Barren Rock, Missouri has the highest concentration, an apparent anomaly in their distribution. Infiltrating the factory, populated by multiple infected, including Max, the group discovers that the Queen infected Victor and his body is being used as a hive to rapidly mass-produce the chips. Fearing being possessed by the chips while in his alien forms, Ben uses the Omnitrix to transform into a new alien that he calls Nanomech, Alex Winter, a hybrid of his human DNA and the chips.
Nanomech flies into Victor's head and battles the Queen, while Gwen, Kevin and Elena fight the infected. As the dormant chips in the factory activate, Nanomech uses the chips' ability to adapt to overwhelm and destroy the Queen, freeing everyone from the chips' control. After apologizing to Victor, Max decides to retire and leave his position as leader to Ben, but Ben refuses as Gwen, Kevin and Elena drive home.
