JUBA, South Sudan — More than two years after South Sudan’s civil war began, its opposition leader landed in the capital, Juba, on Tuesday and was sworn in as vice president, a vital first step in the effort to bring the country back together.
South Sudan, the world’s youngest nation, was born in 2011 to great international fanfare. But shortly after independence, it spiraled into a civil war that killed tens of thousands and displaced more than two million people.
Nearly two years of peace negotiations in Ethiopia’s capital, Addis Ababa, yielded several cease-fires, and recommitments to cease-fires, that were broken almost immediately.
Now the return of the opposition leader, Riek Machar, puts him basically back where he had started, as the official No. 2 to his chief rival, President Salva Kiir.
Still, many analysts doubt that the two will work effectively together after so much blood has been spilled.
As Mr. Machar took his oath of office inside the presidential compound, soldiers were on guard outside. Near the main gate, a truck full of government troops sat a few feet away from a truck weighed down by opposition soldiers. Members of both groups looked glum, sweating under the oppressive heat.
Even before Mr. Machar landed, officials on his side were voicing doubts.
“Juba has not been demilitarized, and aerial bombardment is still happening in some areas of the country,” said Lt. Gen. Simon Gatwech Dual, who flew to Juba on Monday. “So maybe the government is not serious about peace. That could lead us back to war.”
The trouble began in the summer of 2013 after Mr. Machar said he would contend for the leadership of South Sudan’s governing party, the Sudan People’s Liberation Movement.
He was dismissed by Mr. Kiir in July, and fighting erupted in Juba that December, quickly splitting the nation along ethnic lines. Mr. Kiir belongs to the Dinka ethnic group, the country’s largest, while Mr. Machar is a Nuer, believed to be the second largest.
Opposition leaders say that Dinka soldiers hunted down and killed hundreds of Nuer civilians in a few days. Clashes then spread across the country as troops vied for control of South Sudan’s oil fields and regional capitals.
Fighters on both sides have been accused of mass atrocities, including rape, the wanton killing of civilians and the recruitment of child soldiers. The clashes were further complicated by smaller-scale divisions among the country’s ethnic groups, leaving no clear battle lines in the conflict.
In accordance with the negotiations, the opposition leader, Mr. Machar, who had been living in exile at eastern bases in South Sudan and in neighboring Ethiopia, had refused to return without the presence of 1,370 opposition soldiers in Juba, and the last of them arrived last week.
But recent events brought more disruptions: Mr. Machar was scheduled to be sworn in last Monday but postponed his flight to Juba because of disagreements with the government over how many soldiers would accompany him and his chief of general staff, General Gatwech. On Wednesday, the government agreed to allow 195 more opposition soldiers into the capital.
“The delays have been unfortunate,” Mr. Machar said on Tuesday, as he waited to board a plane that would take him to Juba. “I expected to be a little bit earlier, but the organization was problematic. Now I’m going to Juba, and hopefully I’ll take the oath. Then we start forming the transitional government of national unity.”
Despite the long-awaited moment, the mood in Juba was subdued. An idea to organize a public rally welcoming Mr. Machar was discussed, then discarded.
At the swearing-in ceremony, Mr. Kiir said a rally might take place in the future, without specifying when. He also apologized for the peace deal’s slow implementation, and said the country’s leaders were responsible.
“We acknowledge that there are unresolved issues related to the agreement,” he said. “But I promise we will equally resolve those matters amicably.”
While stationed at a rebel base about three months after the war began, Mr. Machar said Mr. Kiir had been “discredited” as a president. “I don’t know what sort of compromise would be reached with him remaining in power,” he added.
But the two sides signed an agreement in August that called for a transitional government in Juba. In February, Mr. Kiir announced that he would restore Mr. Machar as vice president.
An army spokesman, Lul Ruai Koang, said thousands of government troops had been moved to bases outside the city in accordance with the peace plan.
“The army is ready to receive the vice president, as shown by our compliance so far,” he said.
While Mr. Machar’s return to Juba appeared to be a concrete step toward reconciliation, serious questions remained.
Mr. Kiir’s decision in December to divide South Sudan’s 10 states into 28 and appoint new governors has disrupted the negotiations over power sharing. Analysts also warn that after years of bloodshed, a peaceful reintegration of opposition and government soldiers in Juba will be difficult.
General Gatwech said that while he intended to carry out the peace deal, his troops had the right to defend themselves if necessary.
At the United Nations on Tuesday, Secretary General Ban Ki-moonwelcomed the news of Mr. Machar’s reinstatement and urged the “immediate formation” of the transitional government for the country, where United Nations peacekeepers have been sheltering tens of thousands of displaced civilians.
Mr. Ban also announced the appointment of a veteran Nigerian diplomat, Abiodun Oluremi Bashua, to lead an inquiry into an attack two months ago on the United Nations peacekeeping base in the northern area of Malakal that left at least 25 civilians dead and 144 wounded.