This film is set immediately after the events of Greeny Phatom The Movie. The Greeny Phatom characters go to Dr.'s house, stuck listening to his loud cover of Jungle Boogie (as Dr. took DJ lessons). Then, Dr. plays a Smash Mouth song called "Walkin on the Sun", only for Little Guy to smash the disc upon hearing Alien Guy's voice, remarking that time he killed a Gree G. creation. The broken pieces of the disc, Foosch Yo Mung (a parody of Fush Yu Mang), leads to a series of dots, which leads to an Oujia board. Not knowing how to use it, they call Monty Python to help. After the board works, flashes occur, and papers rise as Dr. Beanson says, "That was not fact, nor fiction". They then find the words "Gree Thy Name Is Not Pure", and after saying them, Gree Guy teleports to the house into the universe of The Simpsons, and upon arrival, grabs Bart's father, along with the Scan Passer 9000, with him. Gree Guy teleports to New York, with the Simpsons characters, the Greenytoons characters, and more. Little Guy has a GPS that he has, and tracks down Gree Guy. He found Gree Guy, in a shop. Little Guy catches him, so that Gree Guy can let go of Bart's father, but LG failed, so Gree Guy bought a remote. The characters fight Gree Guy for Bart's father. The Greenies win, and Bart reunites with his father, otherwise, the big ben damaged a bit, the story didn't end. Back at New York, Geo Guy sees that slowly the Big Ben is falling towards Mikey and Little Guy, even Small Pig, they run before the Big Ben went destroyed in small pieces, they discuss about the Big Ben fell, and later in TV, the flashing news are discussing about Big Ben that it is fallen, and persons takes a photo of it, posting it to newspaper. Little Guy, running away from New York, he was taking a trip on the garden, eats his snack, later Wario came and he sees Little Guy, then he spies him, Little Guy sees him, then he began fighting with him, during the fight there was Geo Guy seeing that they are fighting each other, later after the duel, Little Guy went down, then Geo Guy checks Little Guy how he is, he said sick, because of the virus, then Geo Guy fights with Wario, then Wario went down. After the fight, meanwhile, Mario is in the shops, he goes to GameStop, buying a copy of New Super Mario Bros. when he picked it, he sees Bowser buying Bowser's Workshop, for Xbox 360, Mario comes over him, and Bowser turns back to mario, and he kicks out in GameStop, and Bowser stoles the game that Mario buyed, and he puts back to the store, and he made the door unopenable anymore, that only Bowser can open it, when Bowser goes away Mario gets the game again and just now he buys it, later, when Mario came home, when he opens it, he finds out instead of New Super Mario Bros, it was empty!! Just the manual, Mario rages and finds for the cartdige. In 123 Greeny Phatom, Bart visits the city, he sees buildings, Toys 4 Us, but Bart sees a big truck named "Dr Beanson's Pastry", and he is excited to eat them, then he came over Dr. Beason, he said that he's not allowed to eat food, then he strikes him, and Dr. Beanson drives away the truck faster, then Bart picks a car from someone, and when he picks it and goes away some person cries for his car going away from Bart, then when arriving near to Beanson's truck, the jumps and handles the truck, but suddenly Beanson kicks Bart and gets damaged a lot, then he gets bashed from another car, Bart's ears are broken, his arms are almost broken, his legs are broken too, and even the body has revealed his bones, a surgery truck takes him to hospital.
In Little Guy's home, he was sleeping during midnight, later a television started up himself, in the television screen, it has 5 marios, but in creepy quality, calling it "Glitchrio", then Little Guy gets forced himself to wake up, then he stares to the television, and the television says: "OBEY GLITCHRIO, DESTROY THE WATTERSONS!", then Little Guy's eyes went posseded him, then he gets eaten from Glitchrio, then Little Guy screams in terror and it was a dream. Mario rushes for the cartdige of New Super Mario Bros., he sees Bowser holding the cartdige of the game, he said he stole it! He was going to hack the game and replace the player (Mario) into Bowser! Mario runs for it, and duels Bowser, after the duel, Bowser went down and he gives the cartdige to Mario, then he goes to home and tests the game, he said it was fabulous! After Bart failed to get food, he went on a coffee bar, with Little Guy, he sees Dr. PBS without a mustache, due to the Pigs cutted it. Little Guy and Bart waits for the coffee, after he gets into it, he asks for a cup of coffee, after he got it, he suddenly some birds get into the bar and finds it dead, then Kenneth appeared and everyone scared and left the bar, then Little Guy and Bart duels him. In dream logo land, Gree Guy appeared and he makes the Carlco logos and he puts a big 2000, then he invades the Dream Logos world, putting everything into "Gree Guy rocks!" expect the carlco ones. Bart and his mom Marge Simpson was exploring a volcano, he sees some parts of the volcano, then suddenly a portal of the dream logo land, Gree Guy stands on the volcano ground, and he picks Nicole and he attempts to let her fall in the lava, then after it's goodbye quote, he let fall in the lava, and Bart said "NOOOOOOOOOO!!" then he gets Gree Guy, but he disappears, and he cries, but he got kidnapped. King Pig and his pigs are making a new plan to save the world, because Gree Guy is trying to rule the world, King Pig draws the plan in the blackboard, and Helmet Pig sees the pigs, the plan was:
1. Get the weapons. 2. Buy props for war. 3. Kill Gree Guy.
Then pigs prepares to go in war, but they see Gree Guy kidnapping Bart and Mikey. Little Guy gets in Gree Guy's castle, and storms it, after getting to the room where Gree Guy is it at, he started ranting and fighting, after the fight, Little Guy let Mikey and Bart escape the castle, when they escape, the castle shortly collapses. Pixar sees a portal to get in the dream logo land, he sees the Carlco logos, he sees a hammer, which it will be used to break the logos, then he goes in action to break the logos, after he break the logos, he gets teleported back to earth. Mikey went saved, but he was woken in the big ben, and he sees Homsar behind him, and Mikey talks with Homsar, then, Homsar begans singing a song from The Three Mouseketters, then he got misteriously disappeared, and Mikey says "NOOOOOOOOOOOOOOOOOOOO!" and falls to the void, getting on the Final Destination. Mikey is in the Final Destination, King Pig appears, then he does a conversation with him, telling him that Gree Guy is ruling New York and turning into New 123 Gree City, he haves weapons to stop Gree Guy from ruling it, then he joins Mikey and his friends. In the Minimal Rock, a warrior named Beadon is presenting himself, saying "I, i am the supreme warrior of all history, I, BEADON!!!!" then he prepares to fight Pixar, then the duel begins, after the duel he disappears now and he has a soul flying up. Mikey sneaks under at the Big Ben's clock, revealing under that it was Gree Guy breaking the clock, then he runs away for revealing his combattive super villain, after he gets down, Final Boss Man appeared, and he says "Final Boss Man, i, will rule this world with Gree Guy and his evil allies, HAHAHAHAHAHAHHAHA!!!" then he fights with Mikey, after the duel he goes on the Final Boss Castle. Joey was venturing on the fields to beat Dr. Protodisco, after he gets on his castle, he suddenly sees Gree Guy kidnapping Homer Simpson, the actual person of New York, he follows Gree Guy, then suddenly gets grabbed and tried to kill him, then he is dead and his corpse went released, letting his life fail. Mikey had found a red bird, he has no powers, but he is lost from his family, Mikey tells at him that he haves his power to let Red Bird turn into Super Red Bird, so he will save the world from Gree Guy, Mikey gives the magic to him, then he turns into the Super Form, then he also haves snowboards to go fast in the snow mountain, then in the end they get hitted by the walls because Gree Guy made them, then he found a haunted house that Fortran made. In the lava mountain, Little Guy visited it, then he saws Marge's ear, then he pulls her out, revealing his body revived from being not burned in lava for no reason, she said that Bart was killed by Kenneth, because Little Guy was too late from saving him, then they head to Final Boss Castle and they storm it, until now Final Boss Man was revealed to be Gree Guy, because it tought he was a clone of him, then he unleashes his new plan. Meanwhile, Mikey and Pixar are exploring Fortran's Haunted House, then Pixar uses a flashlight to see the rooms, then he found Fortran, and he is coming for they, then Mikey fighting him, but Fortran can't attack because he lives in a pirate game, when Fortran dies he disappears in pixel pieces, then he found a exit to the house. Bowser sees Mario playing with his DS, then he made his DS disappear and he gets in Bowser's lair, fighting him for the last time, after the battle Bowser forgives Mario, then he disappears forever for life, then Mario gets teleported in his house. The televisions twins are in the Superjail, later they found out to break the superjail, then they're trying to find Kenneth, then he began fighting with him, after the battle he is self destructing and the television twins run away, leading to the portal. Gree Guy haves an evil conversation with Marge, he says that he has a Scan Passer 9000 that it has evil power, then he picks his Scan Passer 9000, he melts her, then he picks all of her and he closed it and ran away like a thief, but some of the Greenies, even the piggies noticed it, then they followed Gree Guy, Boba Fett saws Gree Guy with his cup, then he heads to the disney castle, meanwhile they're under the castle, Gree Guy gets to the control room so faster, then he put a chip to let the disney castle fly, then the castle began to fly to...space. Ice Bird on the asteroid saws a disney castle flying, then he flies and tries to get to the door, meanwhile Mikey found Gree Guy's room and they fight for freedom, then after the battle he finally beats up in a Batman The Dark Knight spoof, telling that violence is not the answer, then in the end Ice Bird hits Gree Guy's head, then he gets out to the window, being ended up frozen, then he finds Nicole still liquid, means that she can't get in his normal form anymore, later he joins the super angry birds and the greenies have fun flying in space, even with the liquid Marge, the story went ended with a cinematic tape, that Gree Guy will be once back somedays.
A Dr. PBS clone appears during the process, as well as the Disney Castle. Before the Greenies get choked, Dr. sings his Russian song very loud, and Gree Guy accidentally kills his 1-trillion clones, later getting arrested for it. The group then buys a South Park game.
The Greenytoons characters are on Bart's house, with the Simpsons characters, which are recovering.
Alternative Post-Credits scene/3rd Alt. EndingEdit
Danny Guy is still building his house, but then Little Guy falls on him, causing him to say "HEY I WAS WORKING ON THAT!", then he throws a bomb at him saying "HAVE THIS" and the bomb explodes, causing Little Guy to go back to his house, thus Danny Guy going back to work. This is only shown on a IMAX re-release of Greeny Phatom the Movie from 2014. Spoiler warning: Spoilers end here.
After the cancellation of the original version of Greeny Phatom The Movie, Robert Stainton decided to not make an action film again. However, following the success of Greeny Phatom The Movie and its rereleases, and in preperation of GPTM 2, Stainton teamed up with HiddenLuigi to create a crossover film. HiddenLuigi became the developer of Little Guy Mysteries Movies series and he made this movie. Gree Guy was considered to be the main antagonist and his ally Boba Fett. He put the Simpson family from The Simpsons as the first appearance of the Greeny Phatom sub-series Little Guy Mysteries Movies, it is unknown if they appear on the Greeny Phatom series. The film was first a short film, then adapted into a feature length film then known as Greeny Phatom The Movie 2: Little Guy and The Mystery to New York, but was later split apart in early 2012 into two seperate movies due to long title.
Dr2lol became a helper of this movie and he added a part which Boba Fett betrayed Gree Guy. A shorter version is a special feature in the Blu-ray for Greeny Phatom The Movie.
Later he developed all storyline scene concepts.
The film was originally set for release on Febuary 15, 2013, but it was pushed to July 21, 2013. As a result, the release date for Greeny Phatom The Movie 2 was pushed to a month forward.
After the credits, Little Guy and his friends are at Bart's house, where all of the members of Bart's family recover.
In the 2014 IMAX re-release of Greeny Phatom The Movie, Danny Guy still builds his house, until Little Guy crashes on him and Danny Guy throws a bomb at him push Little Guy back and making Danny Guy still work on it with Peace and Quiet.\
A sequel was planned in 2016 named The Box of Jengo Fett, unlike the first movie of the series, there is no shorter version as special feature on future bluray movies, the movie will discover the mystery of the box from the name of a Boba Fett bounty hounter, "Jengo" Fett.