Third, which represents the majority, is a selective adoption of modernity. In this approach, pesantren creatively integrate modern elements with their traditional practices. This method can be observed in many NU pesantren in Jombang, Krapyak in Yogyakarta, and other areas. They use modern teaching methods and include secular knowledge, while still preserving traditional Islamic texts and teaching styles.
In the 1990s, another type of pesantren emerged, led by individuals with international Islamic networks. These pesantren were more exclusive, focusing less on integrating with local communities and more on maintaining global religious connections. This has led to conflicts between these pesantren and their surrounding communities due to ideological and social gaps.

A Critical Reflection on Pesantren
The evolution of pesantren has resulted in a pluralism within the community. Pesantren no longer reflect a single reality, as was the case during the colonial era. Changes in values, practices, and ideologies have created a more diverse landscape within the pesantren world. Not all pesantren continue to function as religious educational institutions that promote tolerance and align with social realities.
Some pesantren now lack connection with their local communities, instead aligning with external networks and focusing on religious exclusivity. This reality must be carefully examined by scholars, analysts, and pesantren leaders alike. It is important to acknowledge that not all pesantren share the same character or ideology. While some may indeed have links to radicalism due to certain networks or ideologies, the majority of pesantren still work hard to promote inclusive, tolerant Islamic values, even through traditional means.
Given this context, it is unwise to generalize pesantren as either hubs of terrorism or as uniformly traditional and tolerant subcultures. Addressing these issues requires wisdom and critical thinking. Pesantren should not react defensively to terrorism accusations by completely rejecting legal investigations into violent extremists.
Such defensive behavior only strengthens the suspicions that pesantren harbor terrorists. Instead, pesantren leaders should actively clarify their positions to the public, proving that they do not support violence, while also taking a firm stance against terrorism.
By doing so, the public will be able to distinguish between pesantren that espouse radical, violent ideologies and those that promote cultural, substantive Islam—characterized by tolerance and inclusivity.
For those pesantren that embody the latter, there is no need to be overly sensitive to accusations of terrorism or radicalism. They are not part of violent movements. Emotional or excessive reactions to terrorism accusations only benefit the terrorists themselves, giving them a shield to hide behind. Conversely, openness to legal investigations and collaboration with authorities in combating terrorism will diminish the space for radical groups to operate, while reinforcing public confidence that pesantren are not terrorist breeding grounds but instead institutions rooted in tradition and community.
