Sometime in the next several months, if you believe the optimistic noises coming from both sides, the longest-running civil war in the Western Hemisphere will formally come to an end.

For the past three years, the government of Colombia and guerrillas of the Revolutionary Armed Forces of Colombia (FARC) have been negotiating details of a plan to end a conflict that has killed more than 200,000 people since 1964. Last month, they agreed on what they called the most difficult of six elements in a comprehensive peace deal, a process for bringing those responsible for the violence to justice.

That part of the agreement was sealed by a once-unimaginable act: A handshake between Colombian President Juan Manuel Santos and FARC leader Rodrigo Londoño (better known as Timochenko), witnessed by Cuban President Raul Castro in Havana. Further, the two sides promised to finish the agreement within six months, and the rebels committed themselves to disarming 60 days thereafter.

The leftists have taken a beating in the past decade from the Colombian military, backed by billions of dollars in U.S. aid provided through Plan Colombia. If it hadn’t suffered such serious losses, many analysts doubt the negotiations would be where they are today. The U.S. government regards FARC as a terrorist organization, but nevertheless supports the peace negotiations.

Even so, any effort to negotiate an end to half a century of fighting is going to be very, very difficult. There are practical questions about how exactly a deal will be implemented and how much it will cost. And to paraphrase Santos, who must bring a final deal before skeptical voters, there is also a big moral question: To what extent can Colombians live with something less than perfect justice? How much justice are they willing to sacrifice for peace?

To which we might add: How durable is the peace likely to be if there are huge holes in the administration of justice? Or of the entire plan?

As this story points out, guerrilla leaders long have insisted they would not accept prison for engaging in what they regard as a legitimate struggle. And they are far from the only ones accused of crimes and abuses, including killing innocent people. The Colombian military and right-wing paramilitaries are deeply implicated, as well.

To the FARC guerrillas, questions of justice and peace will look much different than they do to the voters Santos needs to convince.

Last month’s agreement lays out the following process for FARC members. Tribunals that include foreign judges will review possible crimes committed during the conflict. Those who confess will face confinement (but not jail) for up to eight years. Those who don’t confess and are found guilty could be jailed for 20 years. For those whose only crime is belonging to FARC, an amnesty is possible.

It will be interesting to see whether Timochenko and other FARC leaders acknowledge any personal responsibility – and how tough the tribunals are. As this Brookings analysis by Vanda Felbab-Brown suggests, Colombian military officers who have fought FARC and oppose the negotiations might actually welcome a lenient approach because the same legal process applies to them.

Colombia attempted a similar demobilization process with the paramilitaries in 2006, only to see many fighters slide back into criminal activities including drug trafficking.

The government and FARC also have agreed on land reform, political participation by the rebels, and how to deal with the drug trade – which has helped fund FARC, and both sides agree must now end. What remains are questions of how the guerrillas will disarm, and exactly how the peace process will be implemented.

As Felbab-Brown points out, land reform will require Santos to fight on behalf of the poor and marginalized against vested interests that have long dominated Colombia. Many of the estimated 8,000 FARC fighters remaining know nothing but war. How do you bring them into the mainstream? Will they even follow their leaders in giving up the fight? And if they do, demobilized paramilitary members could well prey on their old leftist guerrilla enemies.

Colombia, like many Latin American countries, has been hit economically by the crash in commodity prices. But it has built a good financial foundation and is doing better than its neighbors. Still, how does it afford the estimated cost of $30 billion over the next 10 years? Who pays out compensation to the 7 million Colombians who have filed for compensation as victims of the conflict?

And finally, heading into a referendum, Santos will run head on into his predecessor, Álvaro Uribe, who launched the military campaign that weakened FARC.

Santos broke with him to begin the negotiations, and now is the target of Uribe’s wrath. Dealing with what is essentially a spent rebel force will only encourage more violence. Soldiers should not have to face the same tribunals as the guerrillas, and FARC leaders need to pay more heavily for what they did, he says.

To which Santos responds that the whole point of the negotiations is deciding on the line between justice and peace. Regardless of where you put it, “some people will not be satisfied.”