Five years prior to the events of the series, an explosion occurred on Earth, causing microscopic machines called "nanites" to infiltrate the bodies of all its organic life.

At one point, Van Kleiss and Rex are forced to work together to escape the artificial intelligence Zag-RS, who is revealed to be a creation of Caesar's who modeled her voice after their late Mexican mother Violetta.

Back in Hong Kong, Rex encounters and defeats his former boss Quarry, who was given a proposition from Van Kleiss, but was taken to Abysus for punishment after double-crossing him.

In a last-ditch effort to achieve his ultimate goal of becoming a god, Van Kleiss further develops Breach's portal-creating ability, allowing her to travel through time.

In the future, it is revealed that everything has changed drastically since Rex's "disappearance", and he is shocked to meet a woman in charge of Providence who calls herself the "Black Knight."

Rex is sent six months into the future by Breach's abilities, where everything has changed since his "six-month disappearance" and Providence has been taken over by a woman called the Black Knight.

Van Kleiss, who is revealed to have been responsible for Rafael and Violetta's deaths by trapping them inside as the nanite reactor exploded, is taken to Breach's pocket dimension of Greenville, Ohio.

During the conference, show creators "Man of Action" revealed that the crossover would be a special, extended episode of Generator Rex, which aired on November 25, 2011, on Cartoon Network.

[15] Two 3D picture books (featuring cardboard 3D glasses) "EVOs and Heroes," a whole analysis on characters and their abilities and "The Swarm," an adaption of the episode of the same name, where Rex must fight insect E.V.O.s that feed on metal, have also been released.

[15] For beginning readers, the story "Leader of the Pack" is also based on an episode and features Rex and Bobo being captured and locked in an underground prison cell.

[15] In February 2013, IDW Publishing announced a partnership with Cartoon Network to produce comic books and issues based on its properties.