Built in 1975 by Sun Shipbuilding & Drydock Co. as Puerto Rico, the vessel was renamed Northern Lights in 1991 and, finally, El Faro in 2006.

[4] El Faro departed Jacksonville, Florida, under the command of Captain Michael Davidson, bound for San Juan, Puerto Rico, at 8:10 p.m. EST on September 29, 2015, when then-Tropical Storm Joaquin was several hundred miles to the east.

Two days later, after Joaquin had become a Category 4 hurricane, the vessel likely encountered swells of 20 to 40 ft (6 to 12 m) and winds over 80 kn (150 km/h; 92 mph) as she sailed near the storm's eye.

[6] Apache identified wreckage on October 31 "consistent with the [El Faro] cargo ship ... in an upright position and in one piece".

Robert Magee, then president of TOTE, and the ship's crew were praised by United States Air Force general Norton A. Schwartz: "You and your team of professionals showcased the US flag industry at its best.

"[12] After completing her military services in 2006, the ship was transferred by TOTE to its subsidiary company Sea Star Lines and renamed El Faro.

[15] Former crew members of El Faro expressed surprise and shock that the vessel had set sail with a major storm along its planned track.

The staff found that the condition of El Yunque's cargo ventilation system was poor and likely would have been a source of intermittent flooding during rolling in 25–30 ft seas (7.6 - 9.1 meters).

[17] On September 29, 2015, at 8:10 p.m., El Faro left Jacksonville for San Juan, Puerto Rico, carrying a cargo of 391 shipping containers, about 294 trailers and cars, and a crew of 33 people—28 Americans and 5 Poles.

[19] On September 30 at 6:40 a.m. after a review of updated weather data, Davidson and his chief mate decided to alter course slightly southward.

Later, at 11:05 p.m., the third mate called Davidson and told him that maximum winds from Joaquin had increased to 100 mph and that the storm was moving toward El Faro's planned track-line.

Less than twenty hours later, at around 7:30 a.m. on October 1, the Coast Guard received a satellite notification that the vessel had lost propulsion, taken on water—though flooding was contained at the time of the message—and had a 15-degree list.

"[29]: 509 On October 1, WC-130J Super Hercules aircraft of the U.S. Air Force Reserve 53rd Weather Reconnaissance Squadron tried to locate El Faro without success.

[32] Conditions markedly improved on October 4 as Joaquin moved northeast, away from the Bahamas; winds averaged 15 kn (28 km/h; 17 mph) and visibility was unlimited.

[33] Northland and Resolute continued operations overnight with engineers using night vision goggles to take part in the search.

[27][34] The United States Navy provided P-8A Poseidon fixed wing aircraft from Naval Air Station Jacksonville to assist on October 5; three Crowley Maritime tugboats also joined.

[39] A deflated life raft and an unoccupied, heavily damaged lifeboat—one of two aboard El Faro, each capable of carrying 43 people and stocked with food and water for a few days—were also found on October 5.

[42] Senator Bill Nelson of Florida wrote a letter to the agency urging them to look into TOTE's policies regarding severe weather.

[43] On October 14, a $100 million lawsuit was filed against TOTE by a family member of one of the missing crew, citing negligence on the company's behalf in letting a non-seaworthy vessel sail into a hurricane.

[7] On November 16, the wreck was confirmed to be El Faro, and the agency announced it had completed its search of the sunken ship but did not find the VDR.

[49] On January 3, 2016, the NTSB opened the public accident docket on the investigation into the sinking, initially releasing underwater images and video of the vessel.

[50] On April 18, 2016, the NTSB launched a second search for the VDR, using the RV Atlantis, a Navy-owned vessel operated by mariners of Woods Hole Oceanographic Institution.

[51] The Coast Guard's El Faro Marine Board of Investigation completed its final report on September 24, 2017, and published it on October 1 in its document library.

[52] The 199-page Marine Board's Report detailed facts, analysis, and conclusions and made safety, administrative and enforcement recommendations.

Investigators stated that if Davidson had survived the storm, his actions would have been grounds for the Coast Guard to revoke his captain's license.

Coast Guard investigators also noted that TOTE Maritime, El Faro's owner, made several violations regarding crew members' rest periods and work hours, had no dedicated safety officer to oversee the ship, and used outdated, "open air" lifeboats (similar to the types used on older vessels, such as Titanic) instead of the modern-day enclosed survival crafts, among other violations.

[53] The NTSB met in Washington, D.C., on December 12, 2017, to discuss contributing factors to the sinking as well as to "vote on recommendations to address safety issues uncovered during the investigation".

In their final report, the NTSB determinedthat the probable cause of the sinking of El Faro and the subsequent loss of life was the captain's insufficient action to avoid Hurricane Joaquin, his failure to use the most current weather information, and his late decision to muster the crew.

Contributing to the sinking was ineffective bridge resource management on board El Faro, which included the captain's failure to adequately consider officers' suggestions.

Further contributing factors ... were flooding in a cargo hold from an undetected open watertight scuttle and damaged seawater piping; loss of propulsion due to low lube oil pressure to the main engine resulting from a sustained list; and subsequent downflooding through unsecured ventilation closures to the cargo holds.