In January 1987, the MNLF accepted the government's offer of semi-autonomy. The MILF refused to accept the offer. The MILF became the largest separatist group in the Philippines. A general cessation of hostilities was signed in July 1997 but this agreement was broken in 2000 by the government of then President Joseph Estrada. The MILF initially declared a jihad but became more receptive, especially following claims it is linked to the Abu Sayyaf and al Qaeda. A cease-fire accord was signed with President Gloria Macapagal Arroyo
Despite peace negotiations that had appeared to be fruitful and a two year cease-fire, in January 2005 MILF operatives attacked government troops in Maguindanao resulting in at least twenty-three deaths. Led by Abdul Rahman Binago, one hundred MILF rebels surrounded the soldiers and were believed to have executed several wounded. The combined troops of MILF, Abu Sofia and Abu Sayyaf were involved in days of fighting which necessitated government troops using 105 mm howitzers to attack the rebel forces. Thousands of civilians in Maguindanao were forced to leave their homes to avoid danger.
The MILF denied authorizing the attack, and said they were trying to communicate with Binago. A spokesman explained that a relative of Binago had recently been killed by government troops and speculated this might have motivated his activities . The incident, along with a 2003 bombing at Davao airport which the Philippine government blamed on rogue MILF elements, raised speculation that the peace negotiations might be ineffectual in bringing peace to Mindanao if the MILF is unable to control its operatives. The MILF denies ties with terrorist group Jemaah Islamiyah, although Jemaah Islamiyah is believed to have provided them with training facilities in areas they control . The MILF also continues to deny connections with Al-Qaeda, though it has admitted to sending around 600 volunteers to Al-Qaeda training camps in Afghanistan, and that Osama Bin Laden sent money to the Moro region, though the group denies directly receiving any of the money. A new round of fighting occurred from June 28 to July 6, 2006, between the MILF and armed civilian volunteers ("CVOs") under Maguindanao Province Governor Andal Ampatuan who were backed by Philippine Army troops. The fighting began after Governor Ampatuan blamed the MILF for a June 23 bomb attack on his motorcade, which killed five in his entourage. The MILF denied responsibility, but Ampatuan sent police and CVOs to arrest MILF personnel allegedly connected to the attack. Four thousand families were reported displaced by the fighting that followed, which was ended by a cease-fire agreement signed July 10-11.
On July 12, 2007, Islamic militants in Basilan, southern Philippines killed 14 marines, beheading 10 of them, while 9 other marines were wounded and at least 4 rebels were killed. The fight took place as the marines were searching for kidnapped Italian priest, Fr. Giancarlo Bossi (June 10). An MILF spokesman later confirmed that some its members had been involved in the clash, despite the fact the MILF is currently engaged in peace talks with the government. Mohagher Iqbal, the chief negotiator for the MILF, denied that it was responsible for the beheadings or in priest's abduction.On July 19, 2007, despite no ransom being paid for the freedom of Father Giancarlo Bossi, 57 - who was kidnapped on June 10 in Zamboanga Sibugay province, 810 kilometres south of Manila - he was released. He pointed to members of the notorious Abu Sayyaf rebel group as his kidnappers. Authorities blamed a renegade commander of the MILF for Bossi's kidnapping, but it denied any involvement.The MILF said the release of Bossi proved the information they have been feeding to the military -- but which was supposedly largely ignored -- was correct after all. Mohagher Iqbal, MILF information officer and chief negotiator, said had the military listened to them, the incident in Albarka (Tipo-Tipo), Basilan, where 14 Marine soldiers were killed, 10 of them beheaded, could have been avoided. Iqbal said they had been telling the military that Bossi was not in Basilan but they were not heeded, so that it could order troops to operate within rebel territory in Basilan.
On August 4, 2008, the Philippine Supreme Court issued a temporary restraining order, preventing the Government from signing a peace agreement with the Moro Islamic Liberation Front. The Court thus accepted motions by two southern provincial governments that object to the extended boundaries for the Autonomous Region in Muslim Mindanao envisioned in the peace deal.