Later on with the buy-out of Aboitiz Transport System by Negros Navigation using the China-ASEAN Investment Fund loan in 2012 she passed on to the newly merged company 2GO.

She and her sister-ship M/V St. Joan of Arc (ex-Superferry 5/Ferry Hakozaki) were around 40 years old at the time of the sinking, making her one of the longest-serving Philippine-based passenger ships.

On Friday, 16 August 2013, St. Thomas Aquinas departed from Nasipit, Agusan del Norte, on the southern Philippine island of Mindanao.

[7] St. Thomas Aquinas immediately began to take on water, prompting the captain to order an "Abandon Ship" announcement.

[3] Local fishermen saw several flares–a sign of distress–being launched from St. Thomas Aquinas and helped with initial rescue efforts.

[9] On Saturday, 17 August 2013, divers began the process of recovering bodies from the ship, which lay in 30 metres of water, but suspended operations later in the day due to safety concerns.

[9] Maritime accidents in the Philippines are common due to a combination of bad weather, poor maintenance, and lax enforcement of safety regulations.

[7] The Philippine Span Asia Carrier Corporation (operator of Sulpicio Lines) has been involved in five maritime disasters, most notably the 1987 sinking of the ferry Doña Paz that resulted in an estimated 4,000+ deaths.

[13] A Special Board of Marine Inquiry was opened on 23 August in Cebu City, led by Commodore Gilbert Rueras of the Philippine Coast Guard.

[15] The spilled petroleum is expected to contaminate local beaches and mangrove swamps, further damaging Cebu's ecosystem and economy.