Before her promotion to the rank of captain, Hernandez was romantically involved with fellow Starfleet officer Jonathan Archer, However, when Archer was promoted, becoming Hernandez's superior officer, he broke off their relationship. (ENT: "Home")
Hernandez's last assignment prior to taking command of Columbia was on the Republic, under Captain Jennings. When she left the ship, Jennings told her that she could have anything that she wanted. Hernandez ultimately chose to take his chef. (ENT: "Affliction")
Hernandez was promoted to captain in 2154. She was then assigned, along with several other officers, to audit Archer's debriefing subsequent to Enterprise NX-01's return from the Delphic Expanse. After Archer was ordered to take some time off by Admiral Forrest, Hernandez joined Archer as he went rock climbing.
Although Archer was initially reluctant to accept Hernandez's company, as he viewed her as an uncomfortable reminder of the personal sacrifices he had made during his mission to save Earth from the Xindi, Hernandez was successful in assisting Archer in reconnecting with his Humanity, and briefly rekindled their relationship. She saw in him the explorer her father had wanted her to be. (ENT: "Home")
Although Columbia was initially scheduled to launch in June of 2154, engine difficulties prevented the ship's departure from spacedock until November of that year. During that time, Hernandez twice unsuccessfully attempted to recruit Commander Charles Tucker, chief engineer of Enterprise, to her crew. Ultimately, Tucker chose to accept the transfer for personal reasons, and was able to accomplish modifications allowing Columbia to launch.
Shortly afterwards, Hernandez was contacted by Captain Archer, who was requesting Tucker's assistance in repairing Enterprise's warp drive, which had been sabotaged by Klingons. After the successful repairs to Enterprise's engines, Hernandez and her crew joined Enterprise in a dangerous mission into Klingon space to rescue their chief medical officer, Doctor Phlox, and in resolving a crisis involving a virus spreading throughout the Klingon Empire.
Hernandez was given the first name "Erika" in the scripts for "Home" and "Affliction". Indeed, in her first appearance in "Home", she is not named at all, but was described as being in her "late thirties", which would put her birth year at some point during the late-2110s. It goes onto describe her as being, "of slight build and carries herself with an air of confidence."
Hernandez was conceived as a character for Archer to bond with, perhaps romantically, in the episode "Home". The ENT writing staff wanted her to be "equal in stature" to him, in showrunner Manny Coto's words, and to be someone who would respect Archer as well as being respected by him in return. "You know, I think at a certain point, the idea of a second starship commander came about," Coto recalled. 
The idea that she be Hispanic was pitched by Manny Coto, who is Cuban himself and had never seen a Latina starship commander. He thus thought it was high time that such a character be portrayed. 
Manny Coto was involved in the casting of Ada Maris as Hernandez. "I really liked this actress when she came in and read, and I was like, 'That's the one,'" Coto reflected. 
In hindsight, Manny Coto remarked that, if ENT had been renewed for a fifth season, he would have absolutely "loved" to have expanded Hernandez's character. Although he wasn't sure what he would have had her specifically do as the series progressed, he commented, "I really liked her [....] She would have been a terrific additional, you know, with her ship and with Enterprise. It would have been an expansion of Starfleet." 
Hernandez appears in the Star Trek: Enterprise novel Beneath the Raptor's Wing, during which her ship is attacked and incapacitated by Romulan forces, requiring a tow home from Vulcan ships. She is later present at a Coalition Security Council meeting during which Soval announces Vulcan's alternative defense plan. Hernandez finds this plan to be ridiculous and questions it. Later, she has dinner with multiple starship captains at the Lotus Blossom. The novel takes place in the year 2155.
The book Star Trek: Federation - The First 150 Years states Hernandez was promoted to fleet captain prior to the start of the Earth-Romulan War, and in 2156, Columbia and Excalibur were ordered to Starbase 1 in the Algeron system, officially for scheduled maintenance, though the real reason was to protect the base from a potential Romulan attack. The Romulans had declared that Algeron was their property and ordered Humans to leave weeks before. On May 18, five Romulan warbirds attacked the system and jammed communication channels. Hernandez ordered the Excalibur to retreat and warn Starfleet, while Columbia stayed to defend the system. Columbia was lost with all hands, including Hernandez.
In the Star Trek: Destiny novel Gods of Night, Columbia is assigned to escort a convoy when they are attacked by the Romulans, in the year 2156. With the convoy destroyed and Columbia's warp drive offline, Hernandez orders the use of the ship's impulse engines to make a journey to reach the nearest class M planet with any sign of technology, during which the vessel and all aboard experience time dilation effects. While the journey takes twelve years in normal time, the crew of Columbia experiences a passage of only sixty-three days. Arriving in 2168, Hernandez commands the landing party to the planet Erigol that makes first contact with the Caeliar race, liaisoning with Inyx. After efforts by Major Stephen Foyle and other members of the team to use the Caeliar's technology to return Columbia to its original time go badly wrong, the city-ship of Axion, including Hernandez and three of her crew, are relocated in time to the year 1519.
This story is followed up in the Destiny novels Mere Mortals, in which Hernandez encounters Captain William T. Riker and the USS Titan in the year 2381 during a mass Borg invasion of the Alpha Quadrant, and Lost Souls, in which she meets the crew of the USS Enterprise-E and reveals her true nature as a Caeliar, having been granted Caeliar "catoms" after she was the last member of the Columbia crew left alive and in Axion. She is subsequently able to use her catoms to "hack" the Borg Collective – which was created by corrupted Caeliar technology – as she acts as a second Borg Queen, destroying most of the attacking Borg ships and subsequently drawing the rest back to the Azure Nebula, where the Caeliar absorb the Borg Collective into themselves and ascend to a higher level with Hernandez.