The charges are likely to stoke tensions in the oil-rich west African nation, coming one month before the 10th anniversary of hanging of Ken Saro-Wiwa, killed by Nigeria's former military dictatorship after leading protests against Shell's activities in the region.
Mujuhid Dukobo Asari, who faces life in prison if convicted, shouted: "Freedom to my people!" before the charges were read out, and pleaded not guilty before being led out of the heavily guarded courthouse.
The leader of Niger Delta People's Volunteer Force (NDPVF), whose threats to blow up oil platforms have affected global oil prices, was arrested in Port Harcourt, the oil capital of the Niger Delta, after calling for an armed struggle for the independence of his Ijaw people.
He was quoted in the local newspaper as saying: "Nigeria is an evil entity ... I will continue to fight and try to see that Nigeria dissolves and disintegrates."
Although he was placed under heavy security, Mr Asari managed to shout several slogans, including: "Nigeria is a nullity. [President] Obasanjo is a dictator." Saro-Wiwa's execution drew international attention to the role of the oil industry in Nigeria, and forced Western oil companies to adapt their practices to make them more beneficial to local communities and the environment. The Nigerian government is now concerned that Mr Asari and his supporters will again draw international attention to the injustices of the country's oil industry.
The US oil company Chevron closed a station pumping 19,000 barrels a day after being warned of an "imminent threat" from armed militias but later reopened under army protection. Shell also withdrew most of its workers, but managed to maintain its output. Shell's global security chief told the Financial Times the company had been forced to make its own private security arrangements. He said government forces were "totally ineffective".
Mr Asari himself called for calm, and urged his supporters not to sabotage oil production in the delta. The NDPVF's main grievance is that most inhabitants of the Niger Delta live in poverty, even though the 2.4 million barrels of oil a day produced in their region makes Nigeria the eighth-biggest oil exporter in the world. In particular, they want self-determination for the 12 million strong Ijaw, the largest tribe in the region.
Last year, Mr Asari's supporters adopted a high-profile campaign to attack oil installations across the south of the country. Their tactics managed to drive world oil prices above $50 a barrel for the first time ever, forcing President Olusegun Obasanjo to invite Mr Asari to Abuja for talks. Both sides recently eventually signed an agreement, which granted Mr Asari immunity if he disarmed his militia.
Under the deal, the NDPVF has handed in 3,200 weapons, but Mr Asari has never stopped his high-profile campaign for an independent delta. The region has long been a source of tension: many local politicians themselves run armed gangs, which often clash over oil facilities and tap directly into pipelines to siphon gas.
The government said calling for secession in the delta is tantamount to plotting to overthrow the government. The case was adjourned to 10 November. If Mr Asari is convicted, the NDPVF is likely to resume its campaign of violence. This month, two British oil workers were kidnapped by militias in southern Nigeria, but were rescued 24 hours later.
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