They came in waves, ardent Jewish settlers, religious women from central Israel, black-clad followers of Hasidic courts and groups of teenage boys and girls, almost a thousand of them in all.

Crammed into a dozen buses and escorted by the Israeli military, the Jewish pilgrims slid quietly along deserted streets throughout the early hours of a recent morning while the residents of this Palestinian city, a militant stronghold ruled until recently by armed gangs, slept in their beds.

The destination was the holy place known as Joseph’s Tomb, a tiny half-derelict stone compound in the heart of a residential district that many Jews believe is the final burial place of the son of Jacob, the biblical patriarch.

The first group arrived around midnight. Rushing through the darkness into the tomb, they crowded around the rough mound of the grave and started reciting Psalms by the glow of their cellphones, not waiting for the portable generator to power up a crude fluorescent light.

They were praying to be infused with some of the righteousness of Joseph, as well as to be able to return. A gaping hole in the domed, charred roof of the tomb left it partly open to the sky, a reminder of the turmoil of the recent past.

The Palestinians seek Israeli withdrawal from the West Bank and full control over cities like this one. But these religious Jews, spurred on by mystical fervor and the local Jewish settler leadership, are strengthening their bond.

To them this is not Nablus, one of the largest Palestinian cities, with a population of more than 120,000, but the site of the ancient biblical city of Shechem. The tomb, they believe, sits on the parcel of ground that Jacob bought for a hundred pieces of silver, according to Joshua 24:32, an inheritance of the children of Joseph, meaning that its ownership is not in doubt.

Here, the Israeli-Palestinian conflict is boiled down to its very essence of competing territorial, national and religious claims. The renewed focus on what the Jewish devotees call the pull or power of Joseph appears to reflect a wider trend: a move by the settler movement at large away from tired security arguments and a return to its fundamental raison d’être — the religious conviction that this land is the Jews’ historical birthright and is not up for grabs.

“We are as connected to this place as we are to our patriarchs in Hebron,” said Malachi Levinger, a son of Rabbi Moshe Levinger, who founded the first Jewish settlement in that city after the 1967 war. The younger Mr. Levinger had come to the tomb with his wife and three small daughters at 2 a.m.

By day, Nablus is the realm of the Palestinian police, who have largely managed in recent months to restore law and order and to keep the gunmen off the streets. By night the police melt away to avoid encounters with the Israeli forces that still carry out frequent raids.

Under the Israeli-Palestinian agreements of the mid-1990s known as the Oslo accords, Israel withdrew from the Palestinian cities but was assured free access to Jewish holy sites. The army turned Joseph’s Tomb into a fortified post, and a small yeshiva continued to operate there.

But the tomb became a frequent flash point. In 1996, six Israeli soldiers were killed there in a wave of riots by the Palestinian police and militants throughout the West Bank. The second Palestinian uprising broke out in September 2000, and the tomb was the scene of a battle in which 18 Palestinians and an Israeli border policeman were killed; the policeman was left to bleed to death inside. (The settlers note pointedly that the family name of the Israeli, a Druse, was Yusef, Arabic for Joseph.)

To avoid further friction, the Israeli prime minister at the time, Ehud Barak, ordered the army to vacate the tomb and hand it over to the protection of the Palestinian police.

Some declared the tomb an Islamic holy site and painted the dome green; Joseph is considered a prophet in Islam, and his story is related extensively in the Koran. Others believe that the compound is actually the tomb of a Muslim sheik also called Yusef.

Hours after the handover, however, a Palestinian mob ransacked the structure, smashing the dome with pickaxes and setting the compound on fire.

Since then, according to the settlers, the Palestinians have continued to desecrate the tomb, using it as a local garbage dump and sometimes burning tires inside. Though the Palestinian authorities recently cleaned up the tomb, an acrid smell hung in the air, and the walls and floor remained covered in soot.

Since Israel forfeited the site in 2000, Jewish pilgrims, particularly Breslov Hasidim, have visited sporadically, sometimes stealing into Nablus alone in the dark.

The local settlers say they are now working on establishing a routine. Since the beginning of the year, Gershon Mesika, the newly elected mayor of the Samaria Council, which represents settlers in the northern West Bank, has made the resumption of regular visits a priority, coordinating with the army to organize entries at least once a month.

“Our hold on Joseph’s Tomb strengthens our hold on the whole country,” said Eli Rosenfeld, an employee of the council and a former administrator of the yeshiva at the tomb.

Now their goal is to make the visits weekly, then to re-establish the kind of permanent presence that existed before 2000 so that the pilgrims will no longer have to come, as Mr. Mesika put it, “like thieves in the night.”

The recent nighttime pilgrimage, during the Jewish festival of Sukkot, had been organized with precision and was shrouded in secrecy until the last minute, according to a Samaria Council spokesman, David Ha’ivri, not least to avoid hundreds of would-be worshipers’ just showing up.

The operation began just before midnight, as the leaders of the regional council of Samaria, which takes the biblical name for the northern West Bank, gathered at a nearby army base. Boarding a bulletproof minibus, they headed for Nablus. The bus was whisked through a military checkpoint into the city, where the army had secured the tomb in advance and military vehicles were stationed at every junction along the route.

Over the course of the night the buses came and went in convoys according to a tightly organized schedule, bearing pilgrims from the Hebron area, Jerusalem and locations all over Israel. Some of them said they had been on a waiting list for months.

A few of the women cradled babies and toddlers in their arms. Some of the long-skirted teenage girls prayed so intensely that they wept; one rubbed ashes into the palm of her hand.

Growing numbers of soldiers in battle gear joined the worshipers, swept up by the spiritual aura as tea lights flickered on the grave.

As Karlin and Breslov Hasidim surged into the compound, many in fur hats and black silk coats, they spoke excitedly in Yiddish and photographed one another with their cellphones in the sunken courtyard where a mulberry tree once grew. “I come to Joseph, and I feel new,” said one of them, Moshe Tanzer, 22.

In a side chamber that used to house the yeshiva, a lone clarinetist played klezmer music and men sang and danced in circles. Outside, in a hastily erected sukkah, a temporary dwelling for the holiday, pilgrims feasted on sweet and spicy kugel and orange squash.

For those present it was as if the tomb, like Joseph, betrayed by his jealous brothers and sold into slavery in Egypt, had been temporarily redeemed.