Coto joined the writing crew of Enterprise in 2003, when the show was in its third season; his episodes include "Similitude", "Chosen Realm" and "Azati Prime". He became a co-executive producer later that season. In the fourth season he became executive producer of the show, alongside series creators Rick Berman and Brannon Braga.
According to his bio on StarTrek.com, he has been a fan of Star Trek all his life and once wrote a Star Trek comic book. Coto led an effort to further tie in the prequel series with the fictional continuity of the original Star Trek. This concept and much of the restructuring of the show's format was generally well-received by the fanbase, and some fans reported an improvement in the quality of the series in its last season, and credited the effort to an increase in enthusiasm among fans for the struggling show. Other fans, reacting negatively, described the creative shift as "too little, too late," as previous running story arcs were severely reduced or dropped outright with no explanation, in favor of the new direction. Others saw the direction as poorly-executed, in that the "classic" continuity references were seen as superficial and/or contradictory to the spirit of the original series. As is the case with many debates in the Star Trek fan community, this one shows no sign of resolving itself. In any case, ratings for the show continued to decline during Coto's tenure, although few attribute this to Coto, as the ratings had been in a state of general decline since the series' successful debut in 2001.
After that he became co-executive producer on the fifth and sixth seasons of 24, and is currently working as executive producer on the seventh.
Coto has also directed a number of films including Cover-Up starring Dolph Lundgren, Dr. Giggles and Star Kid. He was also a writer, cast member, and co-creator of The 1/2 Hour News Hour, a poorly received right-wing news satire show on the Fox News Channel. With ever-declining ratings, the program was finally cancelled on August 14, 2007 after only 15 episodes.