The troops, with the help of French air strikes, seemed to quickly clear most of the major cities: Timbuktu, Konna and Gao.
France's president, Francois Hollande, flew to the ancient city of Timbuktu on Feb. 2 and was met with adoring crowds who seemed glad to be rid of the menace that they say filled their lives with terror.
Everyone admits the jihadists were a tough foe that easily dispensed with the Malian army last year. Part of what made it so difficult to fight them is the fact that there are people in some cities, like Gao, who sympathize with them and perhaps even support them.
With the exception of France and other west African nations, much of the rest of the international community, Canada included, seems determined to stay out of any significant military involvement in Mali. Canadian Foreign Affairs Minister John Baird warned it could become a quagmire, another Afghanistan.
Inside Mali itself, though, there are glimpses of what is at stake and what may make any attempt to defuse the threat of terrorism a difficult task.
Sense of alienation
Silver-haired and slow-moving Bama Toure is a lifelong resident of Gao. He keeps birds and chickens, and his wife cooks over an open flame.
Just a few hundred yards away, in an open field, the jihadists who ran this city for 10 months carried out harsh and bloody punishments, including cutting off people's hands and feet. But Toure's reaction to the brutality brought upon his neighbours is calm and measured.
He confirms that the jihadists imposed sharia law, but only for those who he says were thieves or adulterers — and Toure seems to have no problem with it.
That reaction doesn't surprise Malian political analyst Adam Thiam, who has spent long hours meeting with people in Gao, trying to understand how militant groups were able to take the city over.
“I was under the impression in talking to some groups that the Salafists [fundamentalist Muslims] were not a problem, that people who had their hands cut off were real thieves," Thiam said.
Thiam said the jihadists tapped into northern Malians' sense of alienation from their own weak government, which is centred in the capital, Bamako, and seems to have no influence or effect outside larger cities.
This alienation stems from ethnic divisions, economic inequality and a belief that southern elites (dominated by black Africans) are not interested in building proper infrastructure in the north, which is largely populated by Tuaregs and Arabs.
"There are people in this community who have never seen a Malian doctor, a Malian teacher or a Malian soldier," Thiam said.
The jihadists arrived in recent years, filling the vacuum with offers of food aid, education and, for young men, a chance to join their militant ranks. It was help the jihadists could provide through the vast amounts of money they make through kidnapping and smuggling.
But they also issued demands at the end of a gun. In Gao, residents say the main group in charge was the Movement for Oneness in West Africa (MUJAO). They work in unsteady alliance with other forces such as Al Qaeda in the Islamic Maghreb (AQIM) and Ansar Dine.
Guns in the mosque
Recently, it was reported that a faction of Ansar Dine’s members was ready to reject extremism and begin negotiations with the Malian authorities.
Local imam Zakaria Yahia Maiga watched jihadists he said were from MUJAO enter his mosque and take over.
"Often, they would come here to pray and they would lay their guns down in front of them, scaring everyone," Maiga said.
They erected stark signs, black with white lettering, warning people that their version of sharia law must be obeyed.
They stayed for months, facing not even the whiff of a challenge from a Malian army that was in disarray.
But now, the army is back.
Malian colonel Didier Dacko says the army will not repeat the mistakes of the past, though he would like the west’s help to ensure the fighters do not simply slip across borders to plot their next attack.
"It might be somewhere else in another country. Somewhere where the situation is profitable to them, another weak state somewhere," Dacko said. "So for this reason I think we have to really take care of all these places that are empty."
Adam Thiam said defeating the jihadists is an arduous task.
"They will not give up the desert. This is where they have invested the most, and they know that an international presence will not be sustainable, and that the [government] of Mali will never have the means to find them," Thiam said.
Thiam suggests what is really needed is a focus on development and aid in northern Mali to reduce the influence of those who preach jihad.
"If you do not invest, you cannot fight the influence of the jihadists. You can kill them, but there will be others to take their place. So development has to go hand in hand with any military effort in order to achieve real security."