A Little Old School tell you the truth.

Unlike the two previous Transformers installments, which were based solely on the script writers' endemic story, Transformers: Dark of the Moon was based on a novel called Transformers: Ghosts of Yesterday, written by Alan Dean Foster. The novel is a prequel to the 2007 film Transformers. It follows the same story structure as Dark of the Moon, being set in 1969, the year of Apollo 11. The story structure differs slightly, though, due to the fact that the novel was written merely as prequel to the first film.

Due to the critically panned Transformers: Revenge of the Fallen, Bay decided to remove the characters called the Twins entirely from Dark of the Moon: "This one really builds to a final crescendo. It's not three multiple endings. One thing we're getting rid of is what I call the dorky comedy. [The twins are] basically gone." Due to fan rumors that the Twins would actually be in the film, the director made a public $25,000 "bet" that the Twins would not be seen in Dark of the Moon.

Bay acknowledged that Revenge of the Fallen was "disappointing to the fans" and stated that he "doesn't want the third one to suck". Bay stated that he wanted Dark of the Moon's final battle to be more geographic and feature a "small group of heroes" like Ridley Scott's war-drama Black Hawk Down.

Bay also decided to include Shockwave because he considers the character "bad" and "He's got a much bigger gun [than Megatron and is] a little bit more vicious." In accordance to The A.V. Club, the film had several minor story inspirations from the 80's cartoon The Transformers, including the usage of a Space Bridge, the "kicking the Autobots out", and a city using as a fortress.

Similar to the previous two installments, the film was told in the human point-of-view to engage the audience. Sam Witwicky's previous love interest, played by Megan Fox, was fired due to her description of director Bay's work ethics on the set of the franchise. Rosie Huntington-Whiteley was chosen to play Sam's love interest in the third installment instead. Bay wanted Sam to have a girlfriend like in the first two films, promising an emotional love story much unlike the previous installments. Actor Shia LaBeouf stated that the additions of Huntington-Whiteley and new characters allows Dark of the Moon to keep the "magic" of the first film.

Dark of the Moon also had numerous Star Trek references, due to the fact that scriptwriter Ehren Kruger was a "big Star Trek geek". The first Star Trek reference is when Sam meets his girlfriend, Carly Spencer at work, and is being introduced to Carly's employer, Dylan Gould, Sam marvels at their workplace: "It's a beautiful building you guys have. Like the Starship Enterprise in here." The second reference is when refugee robots Brains and Wheelie, who live in Sam and Carly's apartment complex, are watching an episode of Trek, Wheelie comments "I've seen this one. It's the one where Spock goes nuts." The third and final reference is when Sentinel Prime activates the Control Pillar, reversing the quote from Spock in Star Trek II: The Wrath of Khan, "The needs of the many outweigh the needs of the few", while the altered version of the quote is "The needs of the few outweigh the needs of the many".

 

but the scene where the found the ark and the events of the ghost of yesterdays still happened at the same time, cause it was confirmed in the prose story Covergence (only avaiable in all 4 issues of the dotm comic adaptation)