UMUAHIA, Nigeria (Reuters) - A secessionist leader seeking independence from Nigeria has been missing since an alleged military raid more than two weeks ago left his house in the city of Umuahia riddled with bullet holes, its windows smashed and doors hanging off hinges.

The disappearance of Nnamdi Kanu, after the raid the army says did not happen, threatens to ignite separatist unrest capable of destabilizing southeastern Nigeria, a region where a million people died in a 1967-70 civil war over the short-lived Republic of Biafra.

Kingsley Kanu, 48, said he was with his older brother Nnamdi, the Indigenous People of Biafra (IPOB) leader, at their family home on the evening of Sept. 14 when soldiers stormed in.

“They were shooting everything they saw,” he said, pointing to bullet holes in walls and windows.

“They came here just to kill everybody,” he said, adding that around 20 IPOB members were shot dead but most of the bodies were taken by soldiers.

Reuters witnesses - a reporter and TV cameraman - on Sept. 27 saw six corpses with bullet wounds in a morgue, who IPOB said were among their members.

Two resembled men in photographs held by weeping relatives who told Reuters their brothers were killed in the raid, though nobody could verify the identities of the four others.

“The military did not raid Nnamdi Kanu’s residence,” a military spokesman told reporters in the capital, Abuja. “Nnamdi Kanu is not in the custody of the military.”

The allegation and denial are the biggest flashpoint of a military deployment in the southeast that began in September.

Civil society groups and analysts say the military presence, last month’s designation of IPOB as a “terrorist organization”, and its leader’s disappearance could prompt the separatists to abandon their policy of non-violence.

President Muhammadu Buhari, a Muslim northerner, made a crackdown on secessionists the focus of his first speech in August after returning from three months of medical leave in Britain.

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He then held talks with armed forces chiefs who days later launched Operation Python Dance, which the military said was intended to reduce violent crime and “secessionist agitations”.

Soldiers with rifles are present across Umuahia, capital of Abia state, in armored vans and at checkpoints where motorists are routinely questioned.

Buhari is already contending with Boko Haram’s jihadist insurgency in the northeast and seeking to maintain a ceasefire with militants in the southern oil-producing Niger Delta.

But some say the former military ruler risks exacerbating the situation, just as militant attacks in the Niger Delta surged last year after troops were deployed.

HEAVY-HANDED?

“The government’s heavy-handed approach will only shore up local support for a radical group that previously struggled to broaden its base,” said Malte Liewerscheidt of global risk consultancy Verisk Maplecroft.

Ryan Cummings, director of Africa-focused risk management company Signal Risk, said the Igbo ethnic group that dominates the region, and has long spoken of being marginalized, felt targeted.

“The government has allowed insecurity to burgeon in other areas of Nigeria without similar deployments,” he said, citing attacks by Fulani herdsmen that have killed hundreds of people in central Nigeria over the last few years.

Tension followed the arrival of troops in the southeast.

Abia’s governor imposed a curfew in the city of Aba last month. Several days of tension between IPOB members and troops led to claims by the group that Kanu’s house had been besieged by soldiers, which the military denied.

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Videos circulating on social media including footage purportedly showing troops in Abia using sticks to flog men stripped to the waist, which the army said it was investigating, have heightened anger.

“The presence of the army scared our people. People spoke about what happened during the Biafran war,” said Onyebuchi Ememanka, a special adviser to the state’s governor who is a member of the opposition People’s Democratic Party (PDP).

“There were no serious security challenges that would justify the deployment of troops,” said Ememanka.

He said he never saw IPOB’s members carrying weapons, though he added that a uniformed national guard and secret service had held parades in the last few weeks, which he called a “new dimension”.

Red, black and green paint - the Biafran flag’s colors - daubed on walls and tree trunks across Umuahia follow calls for a referendum on independence.

Kanu’s release on bail in April, after being held for nearly two years on charges of criminal conspiracy and treasonable offences, brought attention back to the issue.

However, talk of secession among people on the streets of Umuahia mostly hinged on whether or not they had the right to make a democratic choice about their future rather than aligning with IPOB’s belief in a need for a separate state.

Opinions tend to be divided along generation lines, with younger people born long after the war expressing an interest in a referendum while older people who remember the war or grew up hearing stories about the conflict are often wary of even discussing the subject.

However, a pronouncement earlier this year by activists in the northern state of Kaduna that Igbos, who are mainly Christian, should be evicted stirred ethnic tensions. The dispute acted as a lightning rod for frustrations against Buhari, who fought in the civil war on the government side as a young soldier.

A lack of development in the southeast for decades has cemented a belief among Igbos that they have been marginalized.

IPOB ARRESTS

Michael Ogbizi, Abia state police commissioner, said 74 IPOB members had been arrested since Sept. 12 and charged with offences including murder and arson.

Many charges related to the burning down of a police station in mid-September in Aba where nine people died. Ogbizi said police had no records of IPOB members being killed.

An IPOB spokesman denied the group was involved in the fire.

Amid differing opinions about the group’s past conduct, Kanu’s disappearance has created uncertainty about its future.

“If they [the army] have killed him, let them give us the corpse,” said the IPOB leader’s brother, adding that his missing 82-year-old father and 67-year-old mother should be released if they are being held.

Liewerscheidt said if Kanu were to die at the hands of the authorities parallels could be drawn with the origins of the Boko Haram insurgency that began after the death of Mohammed Yusuf, the Islamist militant group’s founder, in police custody.

“This would likely transform IPOB into precisely the terrorist organization the military claims it already is,” he said.