So David Avodraham, who was one of the first to move to Ulpana a decade ago, spent Monday dismantling the kitchen cabinets his father built and loading boxes into a truck bound for storage, leaving little more in the apartment where he lives with his wife and six children than a portrait on the living room wall of a rabbi said to have predicted the Holocaust. “I’m trying to separate my brain from my feelings,” he explained.

But in the next building up the hill, Brad Kitay’s bookcases lined with Talmudic texts sat untouched, his toddler’s toys primed for play. The sole sign of something going on was five small stacks of essentials — baby clothes, a pack of diapers, two bottles, a nail clipper and a few plastic utensils from the girl’s miniature kitchen — piled on the dining room table.

“I can’t bring myself to pack,” said Mr. Kitay, 26, who recently became a rabbi. “My soul is connected with this land.

“It’s not an issue of five buildings,” he added. “It’s whether Jews have a right to live in their homeland.”

Ulpana, founded a dozen years ago in memory of a woman and boy fatally shot by Palestinians, has become the center of a fierce debate here, with right-wing lawmakers threatening to leave Prime Minister Benjamin Netanyahu’s coalition if he follows through on the evacuation, and hard-core settlers vowing to die rather than allow the ouster. Early Tuesday, a West Bank mosque was burned and vandalized, with the words “Ulpana War” scrawled on an outside wall; by nightfall, hundreds of Jews convened at Ulpana for a mass prayer in what they described as a mini-Yom Kippur, invoking the “harsh decree” from the High Holy Day liturgy.

Wednesday morning, shortly after midnight, Dani Dayan, head of the settlers’ Yesha Council, said that leaders in Beit El had reached an agreement with government officials to evacuate peacefully and voluntarily, in exchange for a promise that 300 additional units would be added in Beit El and that Ulpana would not be used as a precedent for policy on settlements elsewhere. Mr. Netanhayu has also offered to remove the buildings from their foundations and move them, rather than demolish them, an engineering feat whose prospects remain uncertain.

Of the more radical settlers presumed responsible for the mosque burning and the threats of violence at Ulpana, he said, “No one can control them.”

More than 1,000 police officers trained in the desert Monday for the operation, aiming to avoid a disaster like the last such evacuation, in 2006, when more than 200 people were injured as thousands protested the demolition of nine houses in the outpost of Amona that were also on private land. While much of the world considers all Jewish settlement in the West Bank illegal, Israel distinguishes between government-approved projects on state lands and so-called outposts built without proper papers or on Palestinian-owned plots; there are as many as 9,000 such units housing perhaps 70,000 people.

“This changes the rules of the game,” said Michael Sfard, a lawyer who brought the case on behalf of one of the Palestinian landowners through the human rights group Yesh Din. “No sound-minded settler will initiate today construction on private land because they would risk significant money.”

For Mr. Netanyahu, generally a settlement supporter, Ulpana is a critical test, particularly in the wake of his expanded power under the broad unity coalition formed last month. He has promised to follow the Supreme Court ruling, but has tried to appease the settlers, culminating in Tuesday’s marathon negotiations that yielded the deal with Beit El’s leadership. “We want to have a situation where that extremist fringe will be isolated,” said a senior aide, speaking on the condition of anonymity because he was not authorized to discuss the situation.

It is an important moment, too, for the settler movement, which has battled to control its radical branches as it grows in influence in mainstream politics. Beit El’s rabbi, Zalman Melamed, declared last week that Ulpana was an occasion for “mesirat nefesh,” a biblical concept of self-sacrifice, and in recent days West Bank youths have warned of violence.

Mr. Dayan joined Mr. Netanyahu in condemning the attack on the Grand Mosque of Jabaa early Tuesday morning, the fourth such religious vandalism in the West Bank in the last 18 months, the police said. After midnight Tuesday, several suspects broke a window of the two-story structure with a recognizable yellow dome and set fire to a carpet inside, the police said.“This time we succeeded in controlling the fire, but I don’t feel this is over,” said Abdul Kareem Bsharat, the mayor of Jabaa, a village of 4,200 people about five miles from both Jerusalem and Ramallah.

The residents of Ulpana, and Beit El more broadly, are mostly middle-class, Orthodox families seen as mainstream and responsible. But in recent days their neighborhood has been flooded with outsiders: well-wishers bringing homemade cakes; a food-charity truck filled with fresh cherries; yeshiva boys poring over sacred texts in a 24-hour vigil; and a small tent city reminiscent of the Occupy movement. Some have strategically placed tires on pathways, ready to be set ablaze to block the police; others stand guard at driveways entering the neighborhood with makeshift weapons.

“I hate it,” said Yael Yosef Chai, 25, one of those to be evacuated. “Youth have inclinations. People who have families are more balanced. They feel humiliated, they feel frustrated, but they will go on.”

In the nearby Palestinian village of Dura al-Qar, the Palestinian owners of the disputed land are also somewhat conflicted: thrilled by the Supreme Court ruling, but dubious of actually getting access to their land, which sits behind a fence and adjacent to other settlement buildings. “After I will put my hand on my land I will talk about it,” said Khaled Yassin, a 47-year-old father of five who said Israeli officials once offered him $16 million for his plot of about three acres. “I don’t want to make dreams before it happens on the ground.”

Harbi Ibrahim Mustafa Hasan, 70, who owns the neighboring plot, recalled riding donkeys through it before 1948 and collecting grapes his family cultivated for eventual sale in Tel Aviv. Mr. Sfard, his lawyer, said that while the evacuation of Ulpana would be a significant political victory, his full goal was “to see Harbi’s family planting new vineyards on their land.”

“I’m not so naïve as to think it will happen in 2012,” Mr. Sfard said. “And when we went to court in 2008 I didn’t think we’d see houses demolished in 2012.”