(written from a Production point of view)
Coto was brought into Star Trek for the third season of Star Trek: Enterprise and wrote several episodes. Showrunners Rick Berman and Brannon Braga were so impressed with his work, and his love for the original Star Trek, that he became the new executive producer for the fourth and final season. However, both men had little choice by then; debuting with a relatively large audience, Enterprise quickly lost viewer-ship and inspired criticism of both the series and its creators, with fans – and, as it turned out after-the-fact, by production staffers as well – criticizing alleged violations in established continuity. With the additional failure of Star Trek Nemesis at the box office in 2002, outspoken critics vehemently clamored for the removal of the "current leadership of the franchise from their positions, including Rick Berman, Brannon Braga, and their entire staff". At the end of the third season of Enterprise, Paramount Television and UPN indicated its cancellation and the apparent end of Rick Berman's tenure as the overseer of Star Trek productions. Whether or not influenced by the vocal criticism and though retaining their official credit, franchise management indeed virtually relegated Berman and Braga to the role of figurehead (admitted as such by Braga in 2007),  and their places were de facto filled for the last season by Coto and Mike Sussman, under whose tenure much of the perceived continuity violation was redressed, aided by writers such as Judith and Garfield Reeves-Stevens, who, like them, had an equally thorough understanding of Star Trek-lore.
His influence helped the show fulfill its stated initial purpose, a prequel to the beloved Star Trek: The Original Series and Star Trek: The Next Generation, through a series of episodes, many of them parts of two- or three-part arcs, that explored some of the missing links in the Star Trek mythology. Episodes focused on what became of the Augments between the Eugenics Wars and the return of Khan, why the Vulcans changed between Enterprise and The Original Series, why the Klingons of The Original Series look different from those in other appearances, how the threat of the Romulans helped to birth the Federation, and who created the transporter. Other homages to earlier Trek incarnations include the appearance of an Original Series-era Constitution-class ship and the Enterprise crew donning original series uniforms, as well as a guest appearance by Next Generation cast member Brent Spiner. While the last season as a whole was generally well received, it did not save the series, as its cancellation had already been decided upon by the studio.
Magnanimously – considering the intense and vicious criticism he had received from the fan base – in 2007 Braga singled out Coto for praise in setting the course straight for the troubled production, "I thought Manny Coto did a great job. One could argue that Enterprise might have been that from the beginning. When I was seeing what Manny was doing it was like "you know what? Maybe this should have been the show from the start"," having added, "If Enterprise had continued, we would have kept going with Manny Coto’s unique vision of the show." 
During Creation Star Trek convention appearances in 2005 and 2009, Coto himself has discussed his involvement with the series, from becoming an unapologetic and unadulterated "Trekkie" in the early 1970s when growing up in Orlando, through being invited by Braga to write for the series, to his decision making as showrunner on the series in Season 4, as seen in the bonus features especially produced by Roger Lay, Jr. for the 2014 Season 3 and Season 4 Blu Ray set releases.
Unsurprisingly, considering Coto's fondness of Star Trek, Coto has cited working on Enterprise as the highpoint of his life – stating he would have "given up a son" if he had been given the chance to work on the franchise from the start, and that he would have died a happy man if he would have been allowed to work on nothing else for the remainder of his life, had the franchise persisted – musing that the more time passes, the more "unreal" and "dreamlike" his memories of the whole experience seem to become.
Career outside Star Trek
Shortly after graduating from the American Film Institute, Coto wrote and directed an episode of Tales from the Crypt. He went on to write and direct the feature films Dr. Giggles and Star Kid. He was a writer and producer on the first season of the 1995 revival of The Outer Limits, and also created the short-lived science fiction series Odyssey 5 for Showtime, whose cast included Tamara Craig Thomas, Leslie Silva, and Peter Weller, the latter two of which Coto worked with again on Enterprise. (Coto subsequently cast Weller again on other series – see below.) Actually, Odyssey 5 was the reason for his subsequent invitation to write for Enterprise as Braga had seen a few episodes. Coto has admitted that the cancellation of Odyssey 5 left him in a state of despair initially, but that his invitation to work on Star Trek instantaneously propelled him in a state of bliss, constituting a disorienting emotional experience.
Following the cancellation of Star Trek: Enterprise, Coto was hired as an executive producer on the FOX series 24 in its fifth season. The cast at that time included Roger Cross, Gregory Itzin, Jude Ciccolella, and Glenn Morshower. During the season, Peter Weller was again cast in a major role, as were Mark Sheppard, Ray Wise, and Tzi Ma. Season six introduced James Cromwell, Alexander Siddig, and Bob Gunton in major roles, as well as Raphael Sbarge and Megan Gallagher. Season seven introduced Annie Wersching and Jeffrey Nordling in regular roles, along with Kurtwood Smith, John Billingsley, and Tony Todd in major roles, and a one-time appearance by Connor Trinneer. A well received series, Coto won a Emmy Award in 2006 in the category "Outstanding Drama Series", supplemented by a 2007 Writers Guild of America Award nomination in the category "Dramatic Series".
After an eighth and final season of 24 (featuring Nazneen Contractor and Necar Zadegan), Coto became an executive producer on the Showtime series Dexter, where he yet again worked with Peter Weller, as well as Raphael Sbarge. That series won Coto in 2011 both an Emmy Award, as well as a second Writers Guild of America Award nomination.
Coto married Robin Trickett on December 27, 2004 in Venice, Italy.
- In the Star Trek: Legacy video game, the player encounters a Poseidon-class destroyer called USS Coto in the first mission of the Star Trek: Enterprise-era campaign. It is likely that the one of the game's producers or programmer named the vessel in honor of Coto's work on the series.
- "Similitude" (Season 3)
- "Chosen Realm"
- "Harbinger" (teleplay only)
- "Azati Prime"
- "The Council"
- "Storm Front" (Season 4)
- "Storm Front, Part II"
- "United" (with Judith and Garfield Reeves-Stevens)
- "The Aenar" (story)
- "Affliction" (story)
- "In a Mirror, Darkly, Part II" (story)
- "Terra Prime" (with the Reeves-Stevenses)
Star Trek interviews
- ENT Season 3 Blu-ray special feature, In a Time of War, 2014
- ENT Season 4 Blu-ray special feature, Before Her Time: Decommissioning Enterprise, 2014