His successor, Abubakar Shekau, vowed to exact revenge on the Nigerian government and a merciless campaign was launched.
In the ensuing Boko Haram killing spree, nearly 30,000 people were killed and more than two million displaced, according to the Council on Foreign Relations’ Nigeria Security Tracker.
A state of emergency was declared in 2013 by then-President Goodluck Jonathan in the northeastern states of Adamawa, Borno and Yobe.
As part of its counterinsurgency operations, the Nigerian military shut down telecommunications in the three states, forcing the fighters to move into Sambisa, a vast forest reserve 60km southeast of Maiduguri that has since become synonymous with the group.
Hundreds of young women have been abducted by the group to become brides to their fighters and in some cases suicide bombers.
Two hundred seventy-six schoolgirls were kidnapped from a Chibok boarding school in April 2014, while another kidnapping in February of last year saw some 110 teenage girls taken from their school in Dapchi.
But it is widely believed that the number of boys and men kidnapped by Boko Haram – most forcibly recruited to fight –over 10 years is much higher.
Abubakar Bala, a 32-year-old shoe mender, has watched his hometown Bama transform from a commercial hub in Borno state to a war-torn husk. His wife was killed when attackers invaded the city in September 2014 and he watched neighbours run over bodies as he fled through the forest.
“Only Allah can heal us. I still don’t know where some of my family members are,” he told Al Jazeera.
Fati Abubakar, a Maiduguri-based photographer, has lost family, friends and neighbours to Boko Haram. She has left Nigeria twice to study overseas and returns to find the situation largely unchanged every time.
“It has been 10 years. We are still waiting – endlessly optimistic but tragically traumatised,” said Abubakar, who has been documenting northeast Nigeria’s slow but resilient journey to normalcy.
“We have waited and waited and waited for Boko Haram to end.”
Yusuf had risen to prominence some seven years before his death, preaching the virtues of an Islamic way of life and encouraging people to turn their back on Western influence.
By 2002, he had established a group he called the Jama’at Ahl as-Sunnah lid-Da’wah wa’l-Jihad, comprising mostly young men galvanised by unemployment, government negligence and inequality.
The group continued to grow, especially in northeastern Nigeria where Borno state is. By 2009, security services had begun to try to shut down the group’s public demonstrations.
It was during one of these altercations that Yusuf was arrested and held by the police, who later announced that he had died under unclear circumstances.
By 2016, a split had formed in the group, which had sworn allegiance to the Islamic State of Iraq and the Levant (ISIL or ISIS) group a year earlier.
While one faction remained under the leadership of Abubakar Shekau, Yusuf’s trusted lieutenant, another faction known as the Islamic State West Africa Province (ISWAP) formed under Abu Musab al-Barnawi, one of Yusuf’s sons.
ISWAP tends to carry out more surgical strikes against military-aligned targets and installations, including one attack in November 2016, which killed seven soldiers and their colonel, Abu Ali, a well-loved commander.
The Shekau faction has moved towards softer targets, said Ryan Cummings, director at Africa-focused political consultancy Signal Risk.
“This came down to one of the core ideological splits within Boko Haram and which played out right at the structures of the Islamic State itself, that Shekau’s penchant for violence against Muslim civilians – which he simply excommunicated due to their failure to live in Boko Haram’s dawlah [Islamic province] – was not justifiable.
“However ISWAP itself has increasingly sought to target civilian interests in armed violence as noted by recent abductions of aid workers but has yet to reach the scale employed by Boko Haram.
“From an operational perspective, ISWAP has demonstrated a more acute capability, often executing surgical raids on military installations in Borno and Yobe states. For Boko Haram, violence has been less sophisticated and defined by armed ambushes on civilian convoys and the employment of suicide bombers against such interests.”
In 2015, President Muhammadu Buhari unseated the incumbent Jonathan, promising to put an end to Boko Haram. Despite multiple claims the armed group has been “technically defeated”, the army still struggles to control the violence.
The fight against Boko Haram has been beset by many drawbacks, including delays to military funding and reports of extrajudicial killings by the army, which has led to the US government refusing to sell weapons to Nigeria.
A coordinated response among neighbouring countries also facing the rebellion has been less than effective.
“This has severely diluted the efficacy of largely unilateral military efforts employed by these countries,” Cummings told Al Jazeera.
“Also, in many of these countries – perhaps including Nigeria – the Boko Haram insurgency is a secondary concern to more pressing security issues occurring elsewhere in their borders, and which has seen a greater allocation of resources and political will.”
In spite of the great gains made against the group, Boko Haram continues to evolve and analysts say the war is far from over.
In fact, an expansion of violence within the Lake Chad basin could destabilise ethnopolitical alliances in and trigger other peripheral security concerns, said Cummings.
“[It could be] similar to what we are witnessing in the insurgency dynamics of Mali and its expansion to neighbouring regions such as Burkina Faso and Niger,” he warned.
The odds may be stacked against Nigeria, but stories of hope are emerging.
Boko Haram barely holds any territory today.
The town of Gwoza, which the group declared as the seat of its caliphate in 2014, has been recaptured by troops and is gradually returning to life, as are other towns in Nigeria, Cameroon, Chad and Niger.
Bala, the shoe mender, has remarried and lives in Maiduguri with his wife. The couple met while staying at the Dalori camp for internally displaced people.
A Civilian Joint Task Force has stepped in to complement efforts by the understaffed army, using rudimentary firearms and machetes to protect their civilian neighbours.
Markets have re-opened and, after three years of playing its home games in northwestern Nigeria, the El-Kanemi Warriors football team has come home to play in Maiduguri.
Local flights from Yola and Maiduguri have started up again and previously shuttered banks are slowly re-emerging.
While many survivors are still grappling with the trauma of living through Boko Haram, more psychosocial support is being made available, lighting flickers of hope in people.
“Borno state, like every other conflict zone in the world, is full of sadness and happiness – gut-wrenching stories one day and awe-inspiring stories the next day,” said Abubakar, the photographer.
“The ability of the human spirit to simultaneously endure tragedies and celebrate triumphs will never cease to amaze me. We have endured for 10 years but are still optimistic that one day it will end.”