The campaign was waged "to weaken the Moro Islamic Liberation Front's capability to undermine the territorial integrity of the Philippines and inflict harm on both government personnel and civilians".

The MILF, however, ultimately rejected the 1996 Final Peace Agreement as inadequate, reiterating a demand for a "Bangsamoro Islamic State", and not just simple political autonomy.

Philippine Army units moved to free the Carmen-Banilasan complex in the province of Cotabato from MILF presence and deny their freedom of movement in the area.

They blocked the Cagayan de Oro-Iligan-Kapatagan national highway and forces under the 303rd BIAF brigade under the command of Abdullah Makapaar occupied the municipal halls of Kauswagan and Munai towns.

The MILF established checkpoints on the Narciso Ramos Highway in Kauswagan, Lanao del Norte and began collecting "toll fees" from those using the roadway.

[9] Furthermore, the concentration of government military assets towards the Mindanao area siphoned off manpower and equipment from the Luzon and Visayas island groups, providing the communist rebellion an opportunity to assert itself.

[10][11] Estrada later ordered that criminal charges against MILF leaders accused of bombings and massacres be withdrawn in an attempt to lure them back to the negotiating table.

The 2000 Mindanao campaign against the Moro Islamic Liberation Front cost the Philippine government Php 6 billion,[12] approximately US$126 million at the September 2016 exchange rate.