A Pasig court has ordered the temporary suspension of the arrest warrant against Moro National Liberation Front (MNLF) leader Nur Misuari in connection with the 2013 Zamboanga siege.

He flew to Manila a few hours after Presidential Adviser on the Peace Process Jesus Dureza presented the suspension order, and was welcomed in Malacañang by President Rodrigo Duterte, whose administration pursues an end to the decades-long separatist rebellion in Mindanao.

• WATCH: Duterte breaks protocol, lets Misuari use presidential podium
• READ: Misuari to play 'key' role in Mindanao peace: Dureza

The residents of Zamboanga, however, are unsettled by the developments. After all, three years after the siege, nearly 14,000 people still live in temporary shelters in transitory sites.

• WATCH: Fear of siege haunting Zambo residents

2013 SIEGE

The government of the Philippines and the Moro Islamic Liberation Front in 2014 signed the Comprehensive Agreement on the Bangsamoro (CAB).

Under the agreement, the rebels would turn over their firearms to a third party which both signatories shall select. The MILF had agreed to decommission its armed wing and the government in turn would establish the Bangsamoro political entity

Allegedly disgruntled after being excluded from the negotiations, the MNLF launched an attack in Zamboanga in September 2013.

In a period of 20 days, the city was a virtual war zone, with gunfire going off, troops and tanks moving, and civilians moving out of their homes.

In the late hours of September 8, soldiers encountered hundreds of armed men in the Rio Hondo District. The next day, a contingent of the MNLF under Habier Malik entered the city.

Malik, who is loyal to Misuari, stormed into the city in an attempt to raise their flag in the capitol.

Aside from Rio Hondo, the armed men occupied the villages of Sta. Catalina, Sta. Barbara, and Talon Talon, where they they took over 200 hostages, most of them civilians.

Authorities also closed the airport and imposed a curfew.

While all this was happening, a spokesperson said Misuari was on the ground in Zamboanga City, but city Mayor Maria Isabel "Beng" Climaco-Salazar said she talked to Misuari who disavowed the attack on her city.

As the days dragged on, the evacuees increased, the number reaching 118,000 residents. They had no recourse but wait for the conflict to end.

When it finally did, the siege left about 200 dead -- including cops, soldiers, rebels, and civilians -- and hundreds more were wounded. Hundreds of MNLF fighters were also arrested.

It left thousands of homes, buildings, and other structures burned to the ground, with the total damage estimated to have been more than $73-million.

• WATCH: Zambo mayor says standoff ‘heartbreaking’

Misuari and his followers were charged for violation of Republic Act Number 9851, also known as the "Philippine Act on Crimes Against International Humanitarian Law, Genocide, and Other Crimes Against Humanity."

On October 8, 2013, Judge Eric Elumba of the Zamboanga City Regional Trial Court Branch 13 issued an arrest warrant against Misuari.

• WATCH: Zamboanga siege leaves scars of war

Misuari then went into hiding.

THE 2001 SIEGE

Many observers note, the 2013 siege in Zamboanga is reminiscent of the situation in the city 12 years before.

In November 2001, Misuari waged war against the government, with his loyal followers attacking an Army headquarters in Jolo, Sulu, in an incident allegedly meant to disrupt the incoming ARMM elections which would have replaced him as governor of the autonomous region borne out of a peace agreement signed with the Philippine government in 1996.

This, after he was ousted as MNLF chair by his colleagues, citing his "incompetent performance," and replaced him with the Committee of Fifteen, the central leadership of the MNLF, a year prior.

The 2001 Jolo attack left some 100 people dead and many others wounded.

Meanwhile in Zamboanga City, 300 Misuari supporters, led by Nur's nephew, Julhambri, took over the Cabatangan government complex and held the residents of the neighborhood hostage.

The elder Misuari initially tried escaped, but was captured by Malaysian authorities days after and was extradited to the Philippines, where he was charged with rebellion in a Sulu court.

In 2008, the charges were dropped.

There are claims, however, that although the charges were dropped, Misuari seem to have carried a grudge against Malaysia for deporting him.

In a 2013 interview, Misuari hit Malaysia for supposedly interfering in the Philippines' internal affairs by acting as third party facilitator to maintain its hold over Sabah.

MILF secretariat head Mohammad Ameen asserted, Malaysia did not volunteer to facilitate the peace talks. Rather, it was the then-president Gloria Macapagal-Arroyo who officially asked Malaysia to facilitate the negotiation.

Then in 2014, according to Malaysian news outfit Malay Mail Online, Home Minister Datuk Seri Ahmad Zahid Hamidi said Misuari was using MNLF men and other groups to intrude into and carry out kidnappings in Sabah, in a bid to raise funds to revive the rebel group's military arm and reassert its influence in southern Philippines.

Zahid said Misuari was believed to be conspiring with individuals said to be part of the Sulu Sultanate, which aims to take over Sabah.

FIGHT NOT OVER

This year, the Duterte administration credited Misuari for helping "very decisively" in the release of Abu Sayyaf captive Norwegian Kjartan Sekkingstad.

Asked why authorities did not arrest Misuari despite the standing warrant against him, Dureza said that the release of Abu Sayyaf hostages is "independent" of the cases pending against him.

With the arrest warrant now suspended, Climaco-Salazar, still serving as mayor of Zamboanga City, said that while she supports the government's peace efforts, the city will pursue cases against Misuari and his men.

She said the case is in the interest of those who died and whose lives changed because of the 21-day siege. Thus, they are standing firm in making Misuari and the MNLF answer for what happened.