In the last few days in Indonesia, inter-communal ugliness has reared its head in way that is major cause for concern. That concern is lighting up mobile phones, Twitter, and Facebook accounts across Indonesia. Indonesians – particularly its middle and professional classes – are outraged to an extent unseen since June 2008 when Islamist militants descended on Jakartans peacefully commemorating Pancasila, Indonesia’s democratic, non-sectarian state creed.

The most recent incidents themselves are terrible. In Banten on Sunday, a mob numbering as many as 1,500 attacked an Ahmadi congregation, resulting in at least three deaths. And a couple days later, in an unrelated incident, three churches were attacked and burned in Central Java over a court’s handling of a blasphemy case.

Of course, to some extent, this is a law enforcement issue. Indonesia has its problems in that regard. But the much bigger problem with these incidents is the cycle of intolerance that encompasses them, a cycle much more familiar in places like Egypt and Pakistan, but which if not checked by firm Presidential leadership in Indonesia, threatens the freedom and fabric, and even territorial integrity of the nation.

The cycle of intolerance begins with political leaders coming under pressure from Islamist forces to enact new laws, regulations or edicts curtailing the free exercise of religion. Second, the leaders cave to these forces or reach a compromise amounting to distinction without difference. Third, vigilantes enforce their preferred interpretation of these government measures by attacking the religious communities in question or otherwise taking the law into their own hands. Fourth, the cycle is complete when the victim is blamed for not better adhering to the restrictions. This leads to even tighter regulation of their religious expression and the cycle beings all over again.

Indonesia is not Egypt, and it’s not Pakistan. It is, indeed, a hopeful society, with a proud tradition of tolerance and pluralism. But there are dangerous Islamist cross currents in Indonesia, some with deep historical roots, some of more recent vintage. These forces are strong enough, and Indonesia’s new democracy still weak enough, that at every turn around recent events in Banten and Central Java, the cycle of intolerance has been on full display.

In 2005, President Yudhoyono was presented with a fatwa from the quasi-official Ulema Council (MUI) condemning Ahmadiyah – a sect many Muslims consider heretical. In 2008, he caved, with an inter-ministerial joint decree “freezing” the sect’s activity.

It is this edict that the vigilantes in Banten took it upon themselves to enforce this past Sunday. As for blaming the victims, Indonesia’s Coordinating Minister for Political, Legal and Security Affairs Djoko Suyanto responded by, in addition to condemning the violence, calling on the Ahmadiyah community to “respect the join ministerial agreement signed in 2008.”

And completing the cycle, Religious Affairs Minister Suryadharma Ali yesterday called on Indonesia’s parliament (DPR) to make the egregious 2008 decree into law in order to prevent more disturbances. The Minister is well-known for his position on the Ahmadiyah – only recently again calling for it to be banned completely. It is hardly believable that his intention is to protect the community.

Ahmadiyah is far more controversial in Indonesia than Christianity. Christians are very much integrated into Indonesian society at many levels and worship freely in churches throughout much of the archipelago. But they, too, have difficulties, most visibly with the construction of new churches. And these difficulties often play out along the same cycle.

President Yudhoyono was a little slow in responding to this week’s attacks, at first merely “regretting” them. Later, he toughened to say, “Every person should be guaranteed protection a safety, whatever his faith, ethnicity, race, political affiliation or profession.” But it’s really even clearer than that. Religious freedom is guaranteed in Indonesia’s constitution. Period. The President should not only speak publicly and much more forcefully on this point, he should do just the opposite of what his Religious Affairs Minister has suggested and overturn the 2008 decree on the Ahmadiyah. While he’s at it, he should ease the approval process for construction of churches and other houses of worship, and see to its implementation.

The cycle of intolerance can only be broken by principled, firm political leadership. And if leaders take a stand, there are things the U.S. can do to help. Yesterday, The Heritage Foundation released a report entitled “Championing Liberty Abroad to Counter Islamist Extremism” with a public event featuring several experts, including the author of the report, Heritage’s own Lisa Curtis, Jim Phillips also of the Heritage Foundation, as well as Hedieh Mirahmadi from the World Organization for Resource Development and Education (WORDE) and Sam Tadros from the Egyptian Union of Liberal Youth.

The Heritage report and event make an explicit connection between the promotion of religious and other universal liberties on the one hand and counter-extremism on the other. The reverse also holds; the erosion of religious liberty feeds extremism. Some Muslim-majority countries, Egypt and Pakistan in particular, are already deep into the repetitive cycle of intolerance. Indonesia is blessed with a new, vibrant democracy and traditions that can break that cycle before it spins out of control. But that is going to take strong political leadership to recognize what is going on and stand up for what’s right.