Dr. Beanson is playing The Legend of Zelda: The Wind Waker on the GameCube. Dr. PBS and Dr. Mother are watching Dr. Beanson play as he tries to kill the enemies. While Little Guy is looking over for his toys (from the first film), Dr. Beanson calls out for him, but he hits his head and falls over. Dr. Beanson gets Little Guy back up on his feet and he talks about looking for his toys. Then Dr. comes around to see The Wind Waker. Then Little Guy gets angry about the video game, then Dr. gets off of it.
Later, the TV gets shaky while Little Guy's pets get scared. The TV then gets glitchy and crashes. Toon Link came out of the TV to look around. Then Toon Link meets Little Guy's pets. The next day, Little Guy and his friends come back to see that the TV is broken, so Little Guy asks about the video game.
More plot coming soon!
Like the show and the first film, some voice actors are text-to-speech and some voice actors are real, such as Santed Sailor and Toon Link.
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. Gabriel Garcia confirmed in July 2012 that since he is a fan of South Park, he wanted to put the short "The Fatrix Reload" (Parody of The Matrix Reload), before the film would start, only to have it shelved with the DVD.
Greeny Phatom The Movie 2 was released on DVD, Blu-ray, and Blu-Ray 3D on January 14, 2014.