Nigerian security forces are searching houses in Maiduguri to find remaining members of an Islamist sect blamed for violence which left hundreds dead.
Bodies have been littering the streets, causing concern about risks to health.
Controversy continues over the death of the leader of the Boko Haram sect, Mohammed Yusuf.
The police say he was killed in a shootout while he was being detained. But an army commander says he was captured, and handed over, alive.
A BBC reporter in Maiduguri says the city is beginning to return to normal, with shops and banks re-opening. But, she says, there are still decomposing bodies on the streets.
She adds that many residents are happy that Mr Yusuf, who led the Boko Haram sect, is dead.
Col Ben Ahanotu, the commander of the operation against the Boko Haram group, said he had personally captured Mr Yusuf, 39, and handed him over to the chief of police.
He said Mr Yusuf was unarmed when caught, hiding in an empty building a short distance from his enclave, and that he gave himself up willingly.
Col Ahanotu said Mr Yusuf had a wound on his arm which had already been treated.
"But he was OK. As I got him alive, I handed him over to the authorities," he said.
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Regional police assistant inspector-general, Moses Anegbode, had earlier told Nigerian television Mr Yusuf had been "killed by security forces in a shoot-out while trying to escape".
Human rights campaigners have alleged Mr Yusuf was shot by the police.
His bullet-riddled body was shown to journalists on Thursday just hours after police said they had captured him in Maiduguri.
The BBC reporter in the city was among journalists shown two films - one apparently showing Mr Yusuf making a confession, the other showing what appeared to be his body, riddled with bullets.
One policeman told AFP Mr Yusuf had "pleaded for mercy and forgiveness before he was shot."
Nigeria's Information Minister Dora Akunyili told the BBC that how Mr Yusuf had died was "a big issue to the good people of this country because Nigeria believes in the rule of law, Nigeria believes in fundamental human rights being respected".
She said his death would be investigated but that the security agencies should be "commended for being able to bring to a stop this killing and destruction in just a few days".
Rights groups have condemned the alleged manner of Mr Yusuf's death.
Human Rights Watch said there should be an immediate investigation into the case, which it has described as an "extrajudicial killing".
Amnesty International said that anyone responsible for or tolerating illegal killings should be brought to justice.
Boko Haram - also known locally as Taliban - wants to overthrow the Nigerian government and impose a strict version of Islamic law.
Troops stormed Boko Haram's stronghold in the north-eastern city of Maiduguri on Wednesday night, killing many of the militants and forcing others to flee.
The violence began on Sunday night in Bauchi state, before spreading to other towns and cities in the north-east of the West African nation. Crowds of militants tried to storm government buildings and the city's police headquarters, but dozens of them were shot dead by security forces.
Several days of gun battles between militants and Nigerian security forces ensued, culminating in the assault on the militant's stronghold.
It is thought more than 300 people have died in the violence - some estimates say 600, although there has been no official confirmation.
The Red Cross said about 3,500 people had fled the fighting and were being housed in their camp.
Police say Mr Yusuf was a preacher from Yobe state, who had four wives and 12 children.
Boko Haram opposes Western education. It believes Nigeria's government is being corrupted by Western ideas and wants to see Islamic law imposed across Nigeria.
Sharia law exists across northern Nigeria, but there is no history of al-Qaeda-linked violence.
The country's 150 million people are split almost equally between Muslims in the north and Christians in the south.
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