This study aims to look at how the strategy for handling terrorism is implemented in this phase by using three analysis variables: strengthening legal infrastructure, strengthening institutional capacity, and implementing policies for handling terrorism. The analysis of these three variables is related to the similarities between the labels used by terrorist groups and the majority religion in Indonesia, namely Islam; and the ongoing democratization in the second ten years of the phase of handling terrorism in Indonesia. By using a qualitative approach and literature studies as well as limited observations from researchers who lived in Indonesia during the research period, the following findings were produced: the Indonesian government's strategy of counterattack against the threat of JI's malignancy experienced a "model disconnection" with previous Indonesian experiences (discontinuity model), which was caused there is a change in the threat of violence which is completely different from the previous threat even though it has a historical connection with past violent groups. Political changes since the enactment of the 1998 Reform so that the ongoing democratization process at that time has slowed the strengthening of legislation and hampered the development of institutional retaliation efforts. There are ideological/religious similarities i.e. Islam, which is held by the majority of the Indonesian population and JI, has created a dilemma for the government in its implementation
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