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Abstract
Separatist conflicts in Southeast Asia, particularly in Aceh and Mindanao, have posed enduring challenges to national integration and regional peace. This study examines and compares the Helsinki Memorandum of Understanding (2005) and the Final Peace Agreement (1996) as frameworks for resolving these long-standing insurgencies in Indonesia and the Philippines. While both agreements aimed to establish autonomy and end armed conflict, their implementation and outcomes diverged significantly. Employing a qualitative comparative case study approach, the research analyzes legal texts, policy documents, and scholarly literature across five key dimensions: legal legitimacy, political participation, fiscal autonomy, security arrangements, and socio-economic impact. The findings indicate that the Helsinki MoU achieved more durable peace through comprehensive legal integration, inclusive governance, and stable fiscal mechanisms. In contrast, the FPA was hampered by weak institutional support, exclusion of critical stakeholders, and financial dependency, leading to continued unrest and eventual renegotiation. These results highlight the necessity of legally grounded, inclusive, and well-resourced agreements in achieving sustainable conflict resolution.
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Copyright (c) 2025 Rafsanjani, Jamaluddin Jamaluddin

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References
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References
Ichwan MN, Salim A, Srimulyani E. Islam and Dormant Citizenship: Soft Religious Ethno-Nationalism and Minorities in Aceh, Indonesia. Islam and Christian–Muslim Relations 2020;31:215–40. https://doi.org/10.1080/09596410.2020.1780407.
Furqan S. Elite Conflict of the Free Aceh Movement. International Journal on Social Science, Economics and Art 2020;10:128–37. https://doi.org/10.35335/ijosea.v10i3.21.
Center E-W. The Free Aceh Movement n.d.
McKenna TM. Muslim autonomy, Political Pragmatism, and the Challenge of Islamist Extremism in the Philippines. Routledge Handbook of Political Islam, Routledge; 2020, p. 115–25.
Sen S. Rebel network theory: The case of Moro Islamic Liberation Front. Conflict Management and Peace Science 2024;41:735–54. https://doi.org/10.1177/07388942231222213.
Kroeker W, Leguro M. Peacebuilding for Peace Processes. Confronting Peace: Local Peacebuilding in the Wake of a National Peace Agreement 2021:279.
Agojo KNM, Teehankee JC. Politics of Ideas and Discourses: Understanding the Ideational and Discursive Struggles in the Formation of the Bangsamoro Autonomous Region in Muslim Mindanao. vol. 23. 2023. https://doi.org/10.59588/2350-8329.1493.
Santos S. Dynamics and directions of the peace negotiations between the Philippine government and the Moro Islamic liberation front. Quezon City 2004;6.
Khan TH, MacEachen E. An alternative method of interviewing: Critical reflections on videoconference interviews for qualitative data collection. International Journal of Qualitative Methods 2022; https://doi.org/10.1177/16094069221090063.
Mammadova G. Financing peace: Examining the effects of economic decentralization within territorial power sharing arrangements 2016.
Järvinen M, Mik-Meyer N. Qualitative analysis: Eight approaches for the social sciences. Sage; 2020.
Bertrand J. Nationalism and ethnic conflict in Indonesia. Cambridge University Press; 2004.
Knott E, Rao AH, Summers K, Teeger C. Interviews in the social sciences. vol. 2. Nature Publishing Group UK London; 2022. https://doi.org/10.1038/s43586-022-00150-6.
Bell C. Peace agreements: Their nature and legal status. American Journal of International Law 2006;100:373–412. https://doi.org/10.1017/S0002930000016705.
Booth A, Martyn-St James M, Clowes M, Sutton A. Systematic approaches to a successful literature review 2021.
Kingsbury D. Peace in Aceh: A personal account of the Helsinki peace process. Equinox Publishing; 2006.
Rüland J, von Lübke C, Baumann M. Religious actors and conflict transformation in Southeast Asia: Indonesia and the Philippines. Routledge; 2019. https://doi.org/10.4324/9780429262364.
Barron P, Burke A. Supporting peace in Aceh: Development agencies and international involvement. vol. 47. Institute of Southeast Asian; 2008.
Schulze KE. The Free Aceh Movement (GAM): anatomy of a separatist organization 2004.
Bacani BR. The Mindanao peace talks: Another opportunity to resolve the Moro conflict in the Philippines. vol. 131. United States Institute of Peace; 2005.