Little Guy has been working on his new clone, but when Gree Guy came and put his own chewing gum into the DNA scanner of the cloning machine, it made a brand-new evil clone named Dark Little Guy. Gree Guy is back for revenge. With help from Dark Little Guy, Gree Guy is in search of the final object of a powerful Triton. The awesome powerful Triton makes any evil plan he controls with it that magically comes true, which happens to be the blue and green toy (which Dr. Beanson purchased from Toys R Us in the first film). When the entire city of 123 Greeny Phatom is put into danger, Little Guy and his friends (Dr. Beanson, Little Guy 2, Geo Guy, Dr. PBS, Green Bob, and Toon Link) need to go on an incredible quest that takes them to Los Angeles inside the alternate live-action universe. In order to get back the toy and save their city in the 'Greenytoons' universe, the gang must retrieve the Triton and transform themselves into a superhero league called 'The GreenyHeroes'.
After the release of Greeny Phatom The Movie in 2002, Robert Stainton confirmed that they might work on a sequel idea. In late 2009, The New York Times reported that the Greeny Phatom team are developing a sequel to Greeny Phatom The Movie. In 2011, it was first announced under the title of "Untitled Greeny Phatom film". Other titles that had been considered include, among others Greeny Phatom: The Second Film, Greeny Phatom The Movie: The Sequel and Greeny Phatom The Movie 2: Little Guy and The Mystery to New York (before getting split apart).
Originally, the film was set to be released on November 9, 2012, but was pushed back to July 6, 2013 to avoid competition with Lincoln, but was later changed to July 18, 2013. In December 2012, it is finally set for a release on August 23, 2013, with Little Guy and The Mystery to New York, another Greeny Phatom movie from 2013, taking its place. The film also includes an original animated short film made by Robert Stainton and Terry Ward, "Crazy Nuts". Promotional television spots for the movie featured the song "Stupid Grin" by Dragonette. The film's main theme is "Fresh" by Devo.
The original soundtrack album was released by Warner Bros. Records in the United States on July 30, 2013 on CD, Vinyl, and digital download. Varèse Sarabande handled distribution of the score from Henderson.