It seemed as if the Ebola crisis was abating.

New cases were plummeting. The president lifted travel restrictions, and schools were to reopen. A local politician announced on the radio that two 21-day incubation cycles had passed with no new infections in his Freetown neighborhood. The country, many health officials said, was “on the road to zero.”

Then Ebola washed in from the sea.

Sick fishermen came ashore in early February to the packed wharf-side slums that surround the country’s fanciest hotels, which were filled with public health workers. Volunteers fanned out to contain the outbreak, but the virus jumped quarantine lines and cascaded into the countryside, bringing dozens of new infections and deaths.

“We worked so hard,” said Emmanuel Conteh, an Ebola response coordinator in a rural district. “It is a shame to all of us.”

Public health experts preparing for an international conference on Ebola on Tuesday seem to have no doubt that the disease can be vanquished in the West African countries ravaged by it in the last year. But the steep downward trajectory of new cases late last year and into January did not lead to the end of the epidemic.

In Sierra Leone, the hardest hit of the countries, the decline leveled off in late January, and the country has reported 60 to 80 new cases weekly since then. Guinea has experienced months of lower-level spread. Even in Liberia, where only a handful of treatment beds remain occupied, responders lament that a health care worker who recently became ill might have exposed dozens of colleagues and patients, and that a knife fight had exposed gang members to the blood of a man who tested positive for Ebola.

“I doubt it will stop just suddenly,” said Dr. Pierre Rollin, an infectious disease expert with the United States Centers for Disease Control and Prevention. “It’s always bumpy, and the bigger the outbreak, the more chance you have a bumpy thing.”

As large epidemics taper off, it is common to find new complications in the effort to reach zero cases. “Oftentimes we find surprises when we get to a low level that were hidden by the epidemic itself early on,” said Dr. William Foege, a former director of the C.D.C. and a leading figure in the eradication of smallpox.

For example, health officials managed to reduce measles drastically in the United States in the 1970s, but it took some time before experts realized that a few travelers per week arriving from other countries were developing the illness, continuing its spread. Importation of measles is again a problem today, and it is suspected as a factor in the current outbreak linked to Disneyland.

Then there is polio, which experts had resolved to eliminate globally by 2000, before wars and unexpected resistance disrupted the plan.

“I don’t think we ever foresaw a time when people would shoot and kill polio vaccinators,” Dr. Foege said, referring to incidents in Pakistan and Nigeria that interrupted inoculation campaigns.

Eliminating smallpox about 35 years ago required a deep understanding of the communities in which it hid. During its last stand, in Somalia, people obscured cases, partly out of embarrassment.

“I think Ebola will turn out to be the same thing,” Dr. Foege said. “The surprises will not be so much scientific as cultural: the ability to hide cases; the desire not to be identified as having Ebola or being in contact with Ebola. Those are the things we have to find out how to overcome.”

That challenge is apparent now in Sierra Leone, where the arrival of infected mariners — combined with a recent easing of anti-Ebola measures, persistent community resistance to containment measures and misunderstanding — has contributed to the surge in the capital. Vice President Samuel Sam-Sumana said Saturday that he had placed himself under quarantine after one of his security officers died of Ebola on Tuesday.

Two wooden boats carrying three sick fishermen arrived at a small wharf in Freetown in early February, cutting short a two-week trip. “The captain was vomiting,” said Mohamed Bangura, 23, a crew member of one boat.

The wharf, Tamba Kula, is an informal settlement where hundreds of people live in shanties made of reclaimed wood and corrugated metal roofs. At the slum’s entrance, a towering sign displays an image of the Statue of Liberty, an advertisement for daily British Airways flights with connections to the United States that were canceled when the Ebola outbreak was declared.

Now, commerce in Tamba Kula is also restricted. Those who contracted Ebola there and nearby — two dozen people since early February — include fishermen, boat cleaners and two women who sold fish.

There are various theories about how the seamen might have been infected and how they spread Ebola to others. Some fishermen delayed reporting their illnesses, stopping instead at an island for treatment with native herbs before coming home to the capital. A few wharf residents who later fell ill thought they had come into contact with contaminated bodily fluids at a shared toilet block that was recently built in Tamba Kula by the aid group Oxfam.

When the cluster erupted at the wharf area — part of a large neighborhood known as Aberdeen, with about 9,000 residents — some Ebola prevention workers were taken by surprise because they had been continuing surveillance efforts. Officials imposed a quarantine, prompting many fishermen to take to the sea to avoid it. The authorities sent out word for them to return.

On a recent afternoon, James Bangura, an official leading the Ebola response in the capital, chastised the deputy harbor master of Tamba Kula for failing to keep arriving fisherman on their boats to be evaluated.

“Once they’re lost and nobody accounts for them, we can’t get to zero,” Mr. Bangura told the man.

“They scatter,” the deputy harbor master responded, but he checked the men from the next boat that arrived.

Outreach teams in recent days made their way over twisting dirt paths filled with garbage, fish bones and shells along seaside settlements in Aberdeen, where narrow passages made it impossible to avoid physical contact with others. The volunteers stopped at dozens of residences. “Nobody sick?” they asked in the Krio language. “You aren’t hiding anybody?”

One night at 11:30, Foday Kamara, a community monitor, walked breathlessly up the road from Tamba Kula. He said he had spent two hours with soldiers chasing down a dozen or so residents who had tried to escape quarantine in the dark. They said that they felt cooped up and that food did not always arrive.

“Ebola work is not easy,” Mr. Kamara said. “I feel like these people, they aren’t ready to end Ebola yet.”

The hard work — by teams of student volunteers, with national and international public health experts — was rewarded, as new cases in Tamba Kula declined.

“I feel like our response was rapid, it was strong, and it appears to have helped,” Dr. John T. Redd, an epidemiologist with the C.D.C., said at the district’s command center in Freetown 10 days ago. On a white board, he had drawn two smiley faces next to the number zero for the previous day’s positive cases.

But the problem was not over. It had moved.

In early February, Abass Koroma, who ran a food grinding shop in Tamba Kula, left there with the help of his wife. His sister had recently died, and he was sick.

Mr. Koroma’s mother, Fatmata Kalokoh, a rice farmer who had traveled to Freetown after her daughter’s death, said her son’s wife had paid a taxi driver about $40 for the three-hour journey back to the family’s village, Rosanda, east of the capital. Her son had refused to go to the hospital in Freetown out of fear, she said. When he arrived in Rosanda, she took him to a traditional healer, who prepared an herbal medicine to help him sleep. Mr. Koroma drank it and began vomiting blood. The next day, he died en route to another village to see another traditional healer.

His death was reported to teams in charge of safe burials, but some villagers said they had touched him while he was sick, thinking that something like a curse had killed him and not Ebola. Mr. Koroma has been linked to the subsequent infections of 42 people in the community, some of whom have died, according to Ebola response officials in the district.

“His wife caused all this,” Ms. Kalokoh said. Now a patient at an International Medical Corps treatment center, she gestured to a treatment tent where her daughter-in-law lay. A survivor working at the center shushed Ms. Kalokoh, saying that it was in God’s hands and that she should not blame anyone.

Every day last week, ambulances bumped over dusty roads, going to Rosanda to carry villagers 45 minutes to the medical center. Two mothers walked weakly to the open doors of an ambulance as their young sons watched, shoulders heaving with sobs. A young girl was taken last Sunday as her mother stood helpless behind candy-striped quarantine tape. The girl, Marie Kamara, died on Friday.

As cases mounted, Dr. Conteh, the district’s Ebola response coordinator, summoned about 125 traditional healers, tribal chiefs and other local leaders. He called for a suspension of traditional practices and warned that criminal summonses were being issued to anyone accused of hiding the sick. Experts fear that such threats will lead more people to go underground.

“The war is still on,” Dr. Conteh told colleagues the next day. “We’re at a critical stage. We can either make or break.”