Gordon was born in Queens, New York, New York. After graduating from Princeton in 1984, Gordon came to Los Angeles with fellow filmmaker Alex Gansa to pursue a career in writing for television. Both broke into the industry with single episodes of ABC's For Hire. Their Spenser work turned industry heads, and the pair joined the Emmy-nominated series Beauty and the Beast as staff writers, and were later named producers.

In 1990, the Gansa-Gordon team was signed to a two-year deal with Witt-Thomas Productions, during which they produced several pilots. One was an ABC project called Country Estates, which caught the attention of famed producer Chris Carter.

Soon after, Carter invited Gordon and Gansa to join The X-Files as supervising producers; Gordon wrote or co-wrote several scripts each season, before departing from the series in 1997 to pursue other projects.

After co-writing one episode of Buffy the Vampire Slayer, Gordon created his own show, the short-lived Strange World in 1999. Strange World went to seed 13 episodes in, but Gordon and Strange World writer Tim Minear's services were quickly snapped up by Buffy creator Joss Whedon on another project: Angel. After two years with Angel, Gordon jumped ship in 2001 for FOX's successful 24, where he would write several episodes in Seasons 1 & 2, then crafted the entire story arcs for Seasons 3 and 4. Gordon temporarily left 24 in the middle of the 2004 season to re-join Minear, this time as co-creator of another FOX series, The Inside. Despite The Inside 's cancellation and short run, talk circulated of including the two Minear-Gordon series, Strange World and The Inside, on a special DVD set sometime in 2006.

Starting in 2006, Gordon became 24's executive producer and show-runner.

It is said that Gordon is now working on a show about the Mossad, the Israeli Secret Service.