[15] The Armed Forces of the Philippines (AFP) received intelligence reports that the MNLF would launch mass operations in Zamboanga City, three days before the incident.

AFP spokesman Col. Ramon Zagala said that according to intelligence reports the MNLF troops were deployed to the coastal barangays (villages) of Rio Hondo, Sta.

[18] In an interview, an MNLF official claimed that the fighters actions was a "pre-emptive response" to a supposed "large" troop movement" of the Army, stating that the group feared that military movement was the prelude to the arrest a high-profile leader of MNLF in the area, such as Nur Misuari.

[19] A commander named Ustadz Habier Malik,[20] who "is a key senior aide of Moro National Liberation Front (MNLF) founder Nur Misuari," is reportedly leading the siege on Zamboanga City.

[21] A navy patrol boat intercepted a large motorboat and eight other smaller vessels carrying armed men near the coastal barangay of Rio Hondo.

[29] Zamboanga City Mayor Isabelle "Beng" Climaco-Salazar later visited the people who fled to different evacuation centers that morning.

The clash between MNLF and the government forces spread throughout the barangay as residents fled their homes while some people could not leave the area due to fear of being caught in crossfire.

[33] During the afternoon, a fire erupted in Barangay Santa Barbara that razed five houses as firefights between the MNLF and the Armed Forces of the Philippines ensued.

Four firetrucks responded, but were delayed, as they needed to have a clearance from the military before entering the area due to the presence of MNLF snipers.

[34][35] Zamboanga City Mayor Climaco finally contacted Nur Misuari through telephone on Thursday.

“While the government is exhausting all avenues for a peaceful resolution of the situation, let it be clear to those defying us that they should not entertain the illusion that the state will hesitate to use its forces to protect our people,” Presidential spokesperson Edwin Lacierda said in a statement.

[36] Vice President of the Philippines Jejomar Binay had spoken by telephone to Nur Misuari, and they agreed on a ceasefire.

[42] Air strikes with 520MG McDonnell Douglas MD 500 Defender attack helicopters and SIAI-Marchetti SF.260 counter-insurgency planes started, firing their guns and rockets against alleged MNLF positions in the city.

[20][47] According to the Philippine Department of Social Welfare and Development, due to the fighting, the number of displaced residents has risen to 110,000, As of 18 September 2013[update], in 35 evacuation centers, such as the Baliwasan Grandstand.

[49] Felipe Rojas, Philippine National Police’s directorate for operations Chief Superintendent, said that the gunmen are being “forced to surrender due to hunger.”[49] Governor Mujiv Hataman of the Autonomous Region in Muslim Mindanao said that most of the gunmen, who surrendered, were unknown and were mostly from “Akbar or Albarka towns in Basilan”.

[51] Government forces gained control over Sumatra Island, which is part of Barangay Talon-Talon and was a strategic landing point used by MNLF fighters.

Cerveza aked that Malik and his closest followers are the "hardcore" fighters of the MNLF and are willing to put their life on the line.

Deputy presidential spokesperson Abigail Valte confirmed the statement of National Defense Secretary Voltaire Gazmin that the conflict in Zamboanga was over.

[57] Combined forces of the Abu Sayyaf, Bangsamoro Islamic Freedom Fighters and the Moro National Liberation Front reportedly attacked the city of Lamitan in Basilan on September 12, 2013.

The Philippine government claimed that the Moro National Liberation Front were using civilian hostages as human shields.

According to the rights group, security forces indiscriminately fired at the MNLF militants holding civilian hostages as human shields.

Magdalo party-list representative Gary Alejano claimed that during the previous administration, if there is a big issue plaguing the government, a diversion will be made.

Zamboanga Representative Celso Lobregat and Autonomous Region in Muslim Mindanao Governor Mujiv Hataman supported calls for an investigation regarding the matter.