It was a first for the International Criminal Court: the request for an arrest warrant for a head of state, Sudanese President Omar Bashir, on charges of genocide, war crimes and crimes against humanity committed in Darfur. But the ICC's attempt to indict Bashir is also a first for the international community - and has occasioned no celebration in Western chancelleries. Governments which have invested seven years' effort in seeking a negotiated transition to peace and democracy in Sudan must now work out how, and if, they can continue to do so once the government has an indicted genocidaire or war criminal at its head.

For the time being, it will be business more or less as usual, in the hope that a formula can be found to prevent a conflict between justice and stability. But the dilemma will become acute in approximately three months' time when the pre-trial chamber of the ICC is expected to rule on Chief Prosecutor Luis Moreno Ocampo's application. It is thought to be a forgone conclusion that the judges will accept the charges of war crimes and crimes against humanity, for which there is overwhelming evidence; and it is probable - but not certain - that genocide will be admitted.

Moreno Ocampo's application has been received ecstatically by the Darfur rebel movements, although more cautiously by civilians at the sharp end of a conflict that has killed hundreds of thousands of its people. The immediate result of the application has been to strengthen Bashir politically as northern opposition parties and the Sudan People's Liberation Movement (SPLM) of South Sudan rally around him to protect the North-South Comprehensive Peace Agreement (CPA) signed by the government and the SPLM in January 2005. It is hard to see Bashir's accomplices handing him over. Darfur rebels tried to overthrow him in May, and failed.

If Bashir begins to feel threatened and hits back, perhaps against United Nations peacekeepers, the hard-won CPA would come under strain. This agreement, which provides a framework for the democratization of the whole of Sudan, ended a 21-year-civil war in which some 2 million people died. After so many years of bloodshed, its implementation has been flawed and difficult. But most of the violence has been halted and an autonomous southern government established. Millions of southerners have returned to their homes. Millions more are enjoying peace for the first time in a generation. A recently approved election law opens the way for the Sudanese to try to remove the regime peacefully, at the ballot box, next year.

Many believe that Moreno Ocampo's move to hold Bashir accountable at this time makes free and fair elections much less likely. Holding them was always going to be an uphill battle. What incentive is there now for Bashir to allow a ballot which, if genuinely fair, would likely see him removed from power and shipped off to The Hague?

Also at stake is a settlement to the Darfur conflict that would allow 2.5 million displaced villagers to return to their homes and rebuild their lives. The Darfur peace process has been dismally neglected - and when not neglected, dismally handled - ever since the Darfur Peace Agreement (DPA) was signed in May 2006 by the Sudanese government and one rebel faction - the wing of the Sudan Liberation Army that was led by Minni Minawi. On this count, therefore, there is nothing to lose, say Moreno Ocampo's supporters. But there is: The Darfur peace process must be revamped and revived, no matter how difficult. The alternative is more insecurity, more chaos, more death.

(So neglected has the DPA been, incidentally, that none of the governments which helped negotiate it has noticed that the agreement has lost its only rebel signatory. Minawi has left the government - and his position as senior adviser to the president - and has returned to the bush, where he is trying to rebuild his military base. His efforts so far have been rebuffed, and he has not announced his defection publicly.)

Human rights lawyers have compared the ICC's move against Bashir to the indictment of Serbian President Slobodan Milosevic. They have argued that Milosevic's prosecution promoted peace and democracy. But Milosevic was weak and there was political cohesion in the action of Western countries who wanted him tried. Compared to Milosevic, Bashir is strong. The African Union, the Arab League, China and Russia all openly oppose the ICC action at this particular time.

Many argue that Moreno Ocampo had no choice but to go where the evidence led him. But Article 53 of the Statute of Rome that set up the ICC requires that prosecutions take into account "the interests of victims." Bashir has presided over a regime marked by recurrent massacre and savage repression. With the CPA still fragile, would the Sudanese people benefit from a diplomatic upheaval that leaves countries like Russia and China all-powerful in Sudan? Would they benefit if the CPA collapses and civil war is reignited?

Moreno Ocampo's move highlights the confused international response to the Khartoum regime - most problematically, the existence of two massive UN peacekeeping operations alongside a criminal process instigated by the UN Security Council, which referred Darfur to the ICC in March 2005, using Chapter VII authority in the UN Charter to compel Sudan to respect the demands of the court. But the dice is cast now. Bashir will be indicted. Moreno Ocampo's curious decision to opt for a public application rather than a sealed warrant has, as Antonio Cassese points out on this page, made his arrest much less likely - as has his equally curious decision to advertise the fact that he had arranged to divert a plane to arrest Sudan's minister of state for humanitarian affairs, Ahmad Haroun, whom the ICC indicted last year.

If Bashir is somehow arrested, then found guilty and imprisoned, it will be a victory for the ICC (if not necessarily for peace and stability in Sudan). But if he continues in power, and possibly is re-elected as president next year, it will be a blow to international justice and an advertisement for impunity.

Julie Flint is co-author, with Alex de Waal, of "Darfur: A New History of a Long War." She wrote this commentary for THE DAILY STAR.