 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.
