-extra dialogue during the news room scene between TV man Melvin Belli (Brian Cox) and the “Zodiac” where Belli asks if there is somewhere he can meet the killer, to which the zodiac responds “meet me on top of the Fairmont Hotel without anyone else.”
-extra dialogue in the same scene where the Zodiac is asked about trying to contact F. Lee Bailey
-extra dialogue again from Belli talking to David Toschi (Mark Ruffalo) and (William Armstrong (Anthony Edwards) at his house about how he was in Africa (which he describes it as “cradle of civilization, fascinating people, beautiful, savage...”) on Safari when the letter came from the Zodiac
-addition of new scene with Toschi and Ken Narlow (Donal Logue) introducing themselves to a Riverside Police officer who says “I hear you have some files for us” to which Toschi jokingly responds “I'll so you mine, you show me yours!” and the title of 2 hours later - Riverside, CA is moved to the beginning of the scene
-in the scene following there is extra info on the victim Sherry Joe Bates including the fact that someone disabled her car, the fact that the particular someone had come back and offered help and Narlow makes a comment about a connection to another case with similar details
-added scene involving Robert Graysmith (Jake Gyllenhaal) coming up to a car and waking up a sleeping Paul Avery (Robert Downey Jr.) and Graysmith spouting off connections between letter that were sent, while Avery acts uninterested - mostly a quirky scene with Downy Jr. showing more character flair
-omission of the line “And shoot the kiddies as they come bouncing out” by Armstrong as he reads the statement back to Donald Cheney (John Hemphill)
-new scene with Armstrong, Toschi, and Marty Lee (Dermot Mulroney) where they talk to a superior via conference call about the details that make Arthur Leigh Allen a prime suspect for being the Zodiac, including physical description, military boot prints, guns, code training in the navy and a barrage of other connectable things; this replaces shot of warrant being slid on a table signed with the voice over “Well, looks like you got your man.”
-an audio homage almost a full minute long which crosses the path of four years over a black screen that includes songs and news stories sound blurbs like Charles Manson, Richard Nixon and Patricia Hearst, before visually going back to the newspaper and the title Four years later
-a little extra Graysmith in anguish when Linda del Buono (Clea DuVall) says “It wasn't Rick”