In March 2014, with Malaysian Prime Minister Najib Razak as witness, the Philippines and the Moro Islamic Liberation Front (MILF) signed a historic pact to end a decades-long secessionist war that had cost at least 120,000 lives.

Two years later, the cornerstone of that deal - the Bangsamoro Basic Law creating an autonomous Muslim region in the restive southern island of Mindanao - has run its full course in Congress.

"It did not make it out of the 16th Congress," Ms Miriam Ferrer, the government's chief negotiator, said in a statement yesterday as Congress held its last session, prior to the start of the campaign season for the May elections next Tuesday.

The peace deal started on strong legs. But a botched operation to arrest Malaysian extremist Zulkifli Hir, alias Marwan, in January last year provided opportunities for opposition lawmakers to stonewall the proposed Bangsamoro law.

More than 40 police commandos who fought hundreds of Muslim fighters, including some from the MILF, were killed in that operation, provoking public outrage and fuelling opposition to the Mindanao peace deal.

But for Ms Ferrer, it was the "sheer indifference and chronic absenteeism" among lawmakers that doomed the Bangsamoro law.

What happens now?

The MILF has said it is not the end of it all, that the next government is legally bound to honour its commitments. But a new administration fresh from securing a mandate from voters is unlikely to touch on such a polarising issue early in its term.

In its current form, the peace deal calls on MILF fighters to lay down their arms and transition into politicians who will lead Mindanao's independent region for Muslims: the Bangsamoro.

The region will have its own police force, a regional Parliament and power to levy taxes.

President Benigno Aquino's successor will have to decide whether to honour these terms or start from scratch. Then, any peace deal will again have to go through lengthy deliberations in Congress, which may take years.

Islamist militants are seizing this opening to sow seeds of discontent.

Ms Ferrer has called the Bangsamoro law a "containment measure against jihadists' extremism". Now, "some groups may head to a different direction, and that's the direction we are all afraid of", she has warned.

It is not even certain now if the 12,000-strong MILF itself will remain on board, as grumblings within its ranks become louder and those who have opposed the deal gain moral ascendancy.

The MILF has had to form a "task force" of Islamic preachers to prevent militant groups that have pledged allegiance to the Islamic State in Iraq and Syria (ISIS) from raiding its ranks.

The immediate threat is from extremist groups that have recently coalesced in an effort to declare a South-east Asia "wilayat", or province, of ISIS.

Then there is the Bangsamoro Islamic Freedom Fighters (BIFF), a breakaway faction of the MILF. It has been raiding remote villages in Mindanao, prompting hundreds of farmers there to arm themselves and form a militia they are calling "Red God's soldiers".

The Moro National Liberation Front (MNLF), of former secessionist champion and now fugitive Nur Misuari, is also at play.

It still commands enough fighters to lay siege to an entire city. In September 2013, it attacked the southern port city of Zamboanga, sparking a three-week-long battle that left at least 244 people dead and 116,000 civilians displaced.

The MNLF has reportedly formed an alliance with the BIFF and the more brutal Abu Sayyaf, which has carried out abductions, beheadings and bombings in the past.

Mr Mohagher Iqbal, the MILF's spokesman, said "it is not the end of the world for us".

Congress' stonewalling of the proposed Bangsamoro law "is only a confirmation of what we have been foreseeing since December last year… We will continue pursuing a settlement", he said.

But for now, with peace again up in the air, the MILF is holding on to its guns.