Jonathan on Tuesday imposed a state of emergency on three northeastern states that are in the eye of the storm -- Borno, Yobe and Adamawa -- to counter what he termed "a rebellion and insurgency by terrorist groups which pose a very serious threat to national unity and territorial integrity."
For the first time, Jonathan, a Christian from southern Nigeria, acknowledged that parts of Borno, the heart of the Islamist insurgency, have been "taken over by groups whose allegiance are to different flags than Nigeria's."
These actions, he said, "amount to a declaration of war and a deliberate attempt to undermine the authority of the Nigerian state."
It was the bleakest assessment of the state's battle with Islamists of the Boko Haram group, which was formed in 2006 and unleashed a campaign of violence in 2009.
Some 1,600 people have been killed in the violence but government officials have generally gone out of their way to downplay the scale of the security threat for political reasons.
Jonathan is already wrestling with tribal militants in the oil-rich Niger Delta in the south and oil theft on an industrial scale that costs the state around $2 billion a year in lost revenue. He was clearly spelling out the danger that Boko Haram, which means "Western education is sacrilege" in the northern Hausa dialect, poses to the country.
This group first made its mark in July 2009, when it engaged in a five-day battle with police in and around the city of Maiduguri, the epicenter of the insurgency. More than 800 people were killed in the violence in which the Islamists wielded machetes, bows and poisoned arrows and a few old rifles.
Despite a military crackdown and the death of its leader, Boko Haram survived and has grown into a well-armed rebel force that since 2010 has been trained by al-Qaida in the Islamic Maghreb.
Al-Qaida's North African branch, led by veterans of the wars in Afghanistan, Iraq and Algeria, is extending its operations across the region and, as the Nigerian bloodletting shows, into sub-Saharan Africa.
In a series of recent attacks involving up to 200 fighters armed with rocket-propelled grenade launchers, tuck-mounted anti-aircraft guns, the Islamists demonstrated firepower and military skills not seen previously, and this has clearly shaken Jonathan's generals.
Jonathan's reference to Boko Haram seizing territory in the north underlines the gravity of the situation because until recently the Islamists hadn't done that. They concealed themselves among the Muslim population of the north.
Nigeria, plagued by official corruption and politicians with their own private militias, has been troubled for years. The country, Africa's most populous nation with 160 million people, is divided more or less equally between Muslims in the north and Christian in the south.
Nigeria's also one of the continent's top oil producers. In recent years much of West Africa has become a major oil-producing zone, which gives the region a strategic importance it didn't have previously have.
Jonathan said he was sending military reinforcements into the three states where the emergency was declared.
He gave no details. But the crackdowns by the military and the security services have been marked by their brutality, and this has driven many Muslims into the arms of Boko Haram.
There also seems to be a growing risk of a religious civil war emerging if Boko Haram isn't crushed.
In April, Christian militants threatened to unleash a "crusade" against the Islamists "in defense of Christianity."
The threat came from the Movement for the Emancipation of the Niger Delta, a coalition of armed groups that's waged an insurgency in the region, the center of Nigeria's oil production, since 2005.
Christians have been a major target of Boko Haram. Scores of churches have been bombed or torched since 2009 and hundreds of Christians killed.
"The bombing of mosques ... Islamic institutions, large congregations of Islamic events and the assassination of clerics that propagate doctrines of hate will form the core mission of this crusade," MEND spokesman Jomo Gbomo declared.