Penelitian ini menjelaskan mengapa ancaman transnasional terorisme tetap ada dan terus berkembang di kawasan meskipun mekanisme kerja sama kontraterorisme Indonesia-Filipina sudah dilakukan. Analisis dalam penelitian ini menggunakan teori kerja sama kontraterorisme oleh Wyn Rees (2006). Hasil penelitian ini menemukan bahwa terdapat perbedaan persepsi ancaman yang signifkan antara Indonesia dan Filipina yang berimplikasi terhadap perbedaan respon kontraterorisme dan eskalasi ancaman pro-ISIS yang berbeda di masing-masing negara. Indonesia menekankan pendekatan criminal justice model. Filipina menekankan pendekatan militeristik. Kedua, kerja sama internal institusi-institusi keamanan Indonesia dan Filipina cenderung bersifat formal daripada substansial. Hal ini dipengaruhi oleh kurangnya rasa saling percaya (trust and reliability), sensitivitas isu kedaulatan teritorial, dan kompetisi di antara institusi-institusi keamanan dalam negeri. Ketiga, kerja sama kontraterorisme AS dengan Indonesia dan Filipina menekankan pendekatan militeristik serta adanya perubahan prioritas keamanan AS yang berimplikasi kepada upaya kerja sama kontraterorisme di kawasan Asia Tenggara. Dengan demikian, upaya penanggulangan ancaman kelompok pro-ISIS di Asia Tenggara melalui kerja sama kontraterorisme Indonesia dan Filipina menjadi kurang optimal.

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This research explains why the transnational threat of terrorism persists and continues to evolve in the region despite the existing counterterrorism cooperation mechanisms between Indonesia and the Philippines. This research uses a qualitative method. The analysis in this research applies Wyn Rees's (2006) theory of Counterterrorism Cooperation. The findings indicate significant differences in threat perception between Indonesia and the Philippines, leading to differing counterterrorism responses and varying level of escalations of pro-ISIS threats in each country. Indonesia emphasizes a criminal justice model approach, whereas the Philippines emphasizes a militaristic approach. Secondly, the internal cooperation of security institutions in Indonesia and the Philippines tends to be more formal than substantive. This is influenced by a lack of mutual trust and reliability, sensitivity to sovereignty issues, and competition among domestic security institutions. Thirdly, US counterterrorism cooperation with Indonesia and the Philippines emphasizes a militaristic approach and a change in US security priorities have implications for counterterrorism cooperation efforts in Southeast Asia. Consequently, efforts to counter the threat of pro-ISIS groups in Southeast Asia through Indonesia and the Philippines' counterterrorism cooperation become less optimal.