The year 2013 saw a continued disparity between conditions in the south and the relatively less developed north, where conflict between Christian and Muslim communities over issues such as land, local administration and religion has since 2009 been deepened by violence from the armed Islamist group Boko Haram. According to analysts, its attacks are motivated by local political and economic matters as well as by religion. Boko Haram reportedly issued video messages in which it used ethnic conflict in other parts of northern Nigeria, such as conflict between settled farmers and nomadic ethnic Fulani herders, in Plateau State, to justify its activities. Boko Haram suicide targets included security force installations; numerous churches were bombed or attacked by gunmen. In past years, the group had targeted schools, but according to reports only when they were unoccupied. From early 2013, however, that tactic changed. In another internet video posting, a Boko Haram leader reportedly claimed the shift was in retaliation for security force targeting of Islamist schools in its crackdown on perceived militants. In one incident in September, at least 40 students at an agricultural college in Yobe state were killed by gunmen. Amnesty International reported in October that at least 70 teachers as well as numerous students had been killed, and many more injured, in targeted attacks in 2013; Boko Haram reportedly claimed responsibility for many of these. Boko Haram has also been accused of widespread abductions of women and children, as well as sexual abuse of women and girls and use of children in hostilities.

In May the authorities declared a state of emergency in the north-eastern states of Borno, Yobe and Adamawa. A military offensive, which included airstrikes by Nigerian planes targeting alleged Boko Haram camps, caused thousands to flee their homes. Many youth joined militias with the aim of dislodging Boko Haram from their neighbourhoods in Maiduguri, the capital of Borno state, or preventing Boko Haram militants displaced by the military offensive from returning to them. Militias reportedly joined members of the military-police Joint Task Force (JTF) at checkpoints in different areas of Borno state to assist in identifying potential Boko Haram militants. The activities of this 'civilian JTF' militia reportedly led in turn to Boko Haram retaliations against militias' communities.

Nigerian security forces were accused of widespread violations, including during security sweeps of nearby communities following Boko Haram attacks. In some instances survivors reported that soldiers accused villagers of collaborating with Boko Haram militants, before killing them and burning their houses.

In April, security forces clashed with Boko Haram near the town of Baga in Borno state, then carried out a house-to-house raid on the town. Satellite images analysed by Human Rights Watch revealed massive destruction. According to reports, between 180 and 200 residents were killed.

Amnesty International reported that during the first six months of 2013, at least 950 people died in JTF detention, while others were 'disappeared'. In August the ICC prosecutor indicated that there was reason to believe that Boko Haram had committed crimes against humanity in northern Nigeria since July 2009; the persistence of violations by security forces during its counter-offensive against Boko Haram, as described above, has led some analysts to call for their inclusion in the ICC probe. In November the authorities extended the state of emergency for another six months.

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