President Abdel Fattah al-Sisi, who took office in June 2014—a year after ousting Mohamed Morsy, Egypt's first freely elected president—leads a country still in crisis. Authorities have imprisoned tens of thousands, effectively banned protests, and outlawed the country's largest opposition group, the Muslim Brotherhood. Courts have sentenced hundreds to death, including Morsy, after unfair trials.

In the northern Sinai Peninsula, fighting between the government and an affiliate of the armed extremist group Islamic State (also known as ISIS) escalated, despite Egypt's commitment of significant additional forces. The government claimed that the army killed thousands of “terrorists” in the Sinai but allowed no independent observers into the conflict area, and residents said the army had killed an unknown number of civilians.

Al-Sisi issued a sweeping counterterrorism law that expanded the authorities’ powers. Law enforcement forces, especially the Interior Ministry's National Security Agency, committed torture and enforced disappearances, and deaths in custody continued. Mass trials mostly targeting Brotherhood members failed to establish individual guilt. At least 3,000 people were charged or sentenced in military courts.

The authorities continued to restrict freedom of expression and association by investigating independent nongovernmental organizations (NGOs), arresting people suspected of being gay or transgender, and prosecuting those accused of defaming religion.

Armed Groups and Counterterrorism

A constellation of insurgent groups throughout Egypt, including the ISIS affiliate, known as Sinai Province, escalated their attacks dramatically, from an average of 30 per month throughout 2014 to 100 per month between January and August 2015, according to the Washington, DC-based Tahrir Institute for Middle East Policy. Though civilians were rarely the target of attacks, in 2015 they were killed at three times the rate of the previous year, the Tahrir Institute found. A June 29 car bombing in Cairo killed General Prosecutor Hisham Barakat, the first high government official to be assassinated since 1990.

The Egyptian government said that its counterterrorism operations in North Sinai killed at least 3,091 “terrorists” between January and July 2015. The government did not allow independent observers into the area of fighting and did not acknowledge any civilian deaths in the Sinai. In September, Egyptian security forces killed 12 civilians, including eight Mexican tourists, in the Western Desert region after apparently mistaking their sightseeing convoy for ISIS fighters. Prosecutors investigating the incident imposed a media gag order four days later.