After independence, Nigeria and Cameroon inherited a border that was never properly settled. Nigeria argued that the relevant boundary predated the 1913 Anglo-German agreement; Cameroon insisted that the 1913 line was definitive. Through the 1980s and 1990s, border skirmishes escalated dangerously. At least 300,000 Nigerians were living in Bakassi at the time, comprising roughly 90 percent of the population. In 1994, facing the real possibility of open war, Cameroon brought the dispute to the International Court of Justice. Eight years of deliberation followed. In October 2002, the ICJ ruled in Cameroon's favor, confirming the 1913 colonial border as the international boundary. Nigerian President Olusegun Obasanjo accepted the verdict grudgingly, attracting fierce criticism at home and abroad. He did not immediately withdraw Nigerian forces from the peninsula.

On 12 June 2006, Nigeria and Cameroon signed the Greentree Agreement, allowing Nigeria to maintain civil administration in Bakassi for two more years while withdrawing at least 3,000 soldiers. The reaction on the peninsula was immediate. A Bakassian delegation threatened to declare independence if the handover proceeded. Separatists, supported by Biafran rebel networks, took to the mangrove creeks with pirate tactics: attacking ships, kidnapping sailors, and launching seaborne raids as far as Limbe and Douala. Nigeria's own Senate declared in November 2007 that ceding Bakassi was illegal, though the declaration changed nothing. On 13 November 2007, clashes between suspected Nigerian soldiers and Cameroon's military left 21 Cameroonian soldiers dead. By the time Nigeria officially withdrew on 14 August 2008, more than 50 people had been killed in the preceding year alone.

For the hundreds of thousands of people living in Bakassi, the conflict was not a matter of sovereignty in the abstract. It was a question of identity, citizenship, and survival. Many residents lacked identification documents. After the handover, they faced a grim choice: renounce their Nigerian nationality, keep it and live as foreign nationals in their own homes, or flee. According to academic Agbor Beckly, Cameroonian police pressured locals to leave. Discrimination drove many families to refuse to register their children as Cameroonians, leaving a generation at risk of statelessness. In 2013, Cameroon launched a crackdown that displaced 1,700 people and provoked Nigeria into threatening military intervention, an intervention that never came. Most remaining separatists eventually accepted amnesty and put down their weapons, but dissatisfaction with Cameroonian governance remained deep.

In 2021, the Biafra Nations League revived the armed struggle, claiming that Bakassi's people identified as Biafran rather than Cameroonian. The BNL launched pirate raids, seized territory, and engaged Cameroonian security forces in running battles across the peninsula's mangroves and waterways. In September 2023, Cameroon carried out airstrikes against BNL camps. Ambushes, bombings, and reprisals continued through 2024 and into 2025, with the fighting drawing in both Cameroonian and Nigerian forces. Abductions of local officials, trade bans, and economic disruption became routine. For the fishing communities and families who have lived on Bakassi for generations, the peninsula remains what it has been since independence: a place where the lines drawn by distant powers cut through the lives of people who had no say in where the borders fell.