Olusegun Obasanjo was elected president in 1999, ending 16 years of military rule, but, as elsewhere, the transition to democracy has released animosities hitherto brutally repressed by dictators.

Nigeria remains intensely corrupt​-​it ranked 143rd out of 183 countries in Transparency International's 2011 corruption index​-​but federal politicians have usually tried to avoid exacerbating regional, ethnic, and religious tensions. Obasanjo was a Yoruba, but drew much support from non-Yorubas, and his bloated cabinet was carefully composed to include at least one minister from each of the country's 36 states. The parties usually choose their presidential candidates alternately from North and South, Muslim and Christian, and pair them with vice presidential candidates of a different religion and region.

Recently this system suffered a partial breakdown. In 2010, President Umaru Yar'Adua, a Muslim, died in office and was succeeded by his Christian vice president, the charmingly named Goodluck Jonathan. In the 2011 presidential election, Jonathan, paired with Muslim vice-presidential candidate Namadi Sambo, beat his Muslim opponent, Muhammadu Buhari, whose running mate was a Christian.

Despite Jonathan's convincing victory​-​and reports from international observers pronouncing the election the fairest in Nigeria for decades (admittedly not a high standard)​-​many Muslim northerners, especially the young, claimed they had been cheated. When the results were announced, there were riots throughout the North, with hundreds killed. Most victims were Christians, but Sambo's house was burned, and traditional Muslim leaders, especially those who counseled restraint, were threatened.

At the state level, politicians have been less careful. Zamfara State governor Ahmed Sani introduced a draconian version of sharia in 1999, and 11 of Nigeria's 36 states followed suit. Muslims, especially women, suffered, but much of the brunt was borne by Christians. Their taxes pay for Islamic preachers, while state governments have closed hundreds of churches. Conflicts over sharia have produced the largest death toll since the Biafra civil war in the 1960s.

The more inchoate mob violence has now been supplemented by Islamist militias. In 2004, a man calling himself Mullah Omar led an uprising in Yobe by a militia called al-Sunna Wal Jamma, nicknamed "the Taliban." While their names had a comic-opera quality, their actions were brutal. Demanding an Islamic state governed by sharia law, they stormed police stations and other government buildings, pulled down the Nigerian flag, raised the old Afghan flag, stole large quantities of weapons, and vowed to kill all non-Muslims. Tens of thousands of people were displaced.

This Taliban has spawned even more vicious offspring. One group is Jama'atu Ahlis Sunna Lidda'awati wal-Jihad (Association Advancing the Prophet's Teachings and Jihad), usually known as Boko Haram, which translates roughly as "Western civilization/education is forbidden." The shorthand name is well chosen since it points to a source of Boko Haram's strength and Nigeria's weakness. Many Muslim children in the North receive no education that could give them work skills. If they go to school, they often attend Islamiyya schools, where they learn to recite the Koran, though in many instances without being able to read or understand it. No one should begrudge young Muslims the opportunity to learn their sacred texts, but many learn little else. Since they have few practical skills and live in an economically depressed area, millions end up unemployed and vagrant. In turn, these angry youths become the radicals' recruits. They attack schools and government offices, and so the cycle repeats.

Boko Haram attacks anyone, Christian or Muslim, who rejects its views. In July 2009, it attacked police stations, prisons, schools, churches, and homes, burning everything in its path. Its violence spread through Borno, Kano, and Yobe states, particularly targeting Christians. Many were forced, under threat of death, to renounce their faith; 700 people were killed in the town of Maiduguri alone.

In August 2011, Boko Haram bombed the U.N. headquarters in Abuja, Nigeria's capital, and killed 23 people. Christmas is a focal time for attacks by Islamic extremists. This past Christmas, churches were bombed in Jos, Kano, Damaturu, and Gadaka. A blast at St. Theresa Catholic Church in Abuja killed 35 and wounded many others. These coordinated attacks, in the Northeast, North, and center of the country, reveal an increased sophistication.

In January, Boko Haram warned the millions of Christians living in the North that they had three days to leave or would be attacked. Gun and bomb attacks in Kano killed at least 186 people and put thousands to flight. In 2011, Boko Haram killed about 500 people; in just the first month of 2012, it killed over half that many.

Nigeria's conflicts are complex, but Boko Haram's explicit targeting of Christians is undeniable. Leader Abubakar Shekau has declared: "Everyone knows that democracy and the constitution is paganism. .  .  You Christians should know that Jesus .  .  . is not the Son of God. This religion of Christianity you are practicing is not a religion of God​-​it is paganism. .  .  . We are trying to coerce you to embrace Islam, because that is what God instructed us to do."

Boko Haram has many layers, from a disciplined core to a stable of alienated youth, but its center is now linked to other terrorists. On August 9, 2009, the group explicitly aligned itself with al Qaeda, and reportedly some of its personnel have trained in Mali with Al Qaeda in the Islamic Maghreb (AQIM). In turn, AQIM says it will give Boko Haram "whatever support we can in men, arms, and munitions to enable you to defend our people in Nigeria." Boko Haram is now morphing into something like Somalia's al-Shebaab.

Still, for all its problems, Nigeria is not Somalia. Moreover, since the Persian Gulf is looking ever more precarious, and Nigeria lies near the center of one of the world's most significant hydrocarbon areas, it should draw the attention of even the most flinty-eyed realists.

Fortunately, the U.S. Africa Command (AFRICOM), especially its program of regional counterterrorism partnerships, was formed with such situations in mind. Nigeria's security forces need equipping to counter Boko Haram and its imitators, and training to do so without the brutality that would feed their recruitment. While it is facile to link international terrorism with poverty, Nigeria's -millions of marginalized Muslim youth are easy recruits to violence. Supporters of both hard and soft power can find common cause in this effort​-​and together hope that a president named Goodluck will live up to his name.

Paul Marshall is a senior fellow at the Hudson Institute's Center for Religious Freedom and coauthor, with Nina Shea, of the just-released Silenced: How Apostasy and Blasphemy Codes are Choking Freedoms Worldwide.