In 2003, Lorenzo di Bonaventura was interested in making a film about advanced military technology; Hasbro's Brian Goldner called him and suggested to base the film on the G.I. Joe toy line. Goldner and Bonaventura worked together before, creating toy lines for films Bonaventura produced as CEO of Warner Bros. Goldner and Bonaventura spent three months working out a story, and chose Michael B. Gordon as screenwriter, because they liked his script for 300. Bonaventura wanted to depict the origin story of certain characters, and introduced the new character of Rex, to allow an exploration of Duke. Rex's name came from Hasbro. Beforehand, Don Murphy was interested in filming the property, but when the Iraq War broke out, he considered the subject matter inappropriate, and chose to develop Transformers (another Hasbro toy line) instead. Bonaventura felt, "What [the Joes] stand for, and what Duke stands for specifically in the movie, is something that I'd like to think a worldwide audience might connect with."
By February 2005, Paul Lovett and David Elliot, who wrote Bonaventura's Four Brothers, were rewriting Gordon's draft. In their script, the Rex character is corrupted and mutated into the Cobra Commander, whom Destro needs to lead an army of supersoldiers. Skip Woods was rewriting the script by March 2007, and he added the Alex Mann character from the British Action Man toy line. Bonaventura explained, "Unfortunately, our president has put us in a position internationally where it would be very difficult to release a movie called G.I. Joe. To add one character to the mix is sort of a fun thing to do." The script was leaked online by El Mayimbe of Latino Review, who revealed Woods had dropped the Cobra Organization in favor of the Naja / Ryan, a crooked CIA agent. In this draft, Scarlett is married to Action Man but still has feelings for Duke, and is killed by the Baroness. Snake-Eyes speaks, but his vocal cords are slashed during the story, rendering him mute. Mayimbe suggested Stuart Beattie rewrite the script. Fan response to the film following the script review was negative. Bonaventura promised with subsequent rewrites, "I'm hoping we're going to get it right this time." He admitted he had problems with Cobra, concurring with an interviewer "they were probably the stupidest evil organization out there [as depicted in the cartoon]". Hasbro promised they would write Cobra back into the script.
In August 2007, Paramount Pictures hired Stephen Sommers to direct the film after his presentation to CEO Brad Grey and production prexy Brad Weston was well-received. Sommers had been inspired to explore the G.I. Joe universe after visiting Hasbro's headquarters in Rhode Island. The project had found the momentum based on the success of Transformers, which Bonaventura produced with Murphy. Sommers partly signed on to direct because the concept reminded him of James Bond, and he described an underwater battle in the story as a tribute to Thunderball. Stuart Beattie was hired to write a new script for Sommers's film, and G.I. Joe creator Larry Hama was hired as creative consultant. Hama helped them change story elements that fans would have disliked and made it closer to the comics, ultimately deciding fans would enjoy the script. He persuaded them to drop a comic scene at the film's end, where Snake-Eyes speaks. To speed up production before the 2007–2008 Writers Guild of America strike, John Lee Hancock, Brian Koppelman and David Levien also assisted in writing various scenes. Goldner said their inspiration was generally Hama's comics and not the cartoon. Sommers said had it not been for the rich backstory in the franchise, the film would have fallen behind schedule because of the strike.
