TEL AVIV, Israel — Israel’s top military commander sat on the edge of his bed, talking on the phone, rubbing his forehead. The bedroom door was closed, muffling the Saturday clink and giggle of his children at lunch. His chief of operations was on the gray, secure phone, the line that rang louder and sharper and made his heart beat fast.

The report came from the war room: The bomb was falling.

Lieutenant General Moshe Yaalon stared at the tiles on his floor, working out two plans: 1) If they die. 2) If they don’t. The bomb — the one he had been arguing over and deliberating all day — was plunging 10,000 feet from an Israeli F-16 toward a Palestinian house in the Gaza Strip, where guests sat, eating rice and boiled chicken. General Yaalon was hoping, he recalled in an interview, that it would be their last lunch. With targeted killings, it was rarely that simple.

It was September 6, 2003, a time — much like today — of open warfare between Israel and Hamas, which Israel, America, and Europe have labeled a terrorist group, and which now controls the Palestinian Authority. Eight Hamas leaders had gathered to plan terrorist attacks, Israeli intelligence claimed.

“It was like bin Laden, Zarqawi, and Zawahiri in a meeting and having the capability to hit them,” Lieutenant General Dan Halutz, then the air force chief and now the military chief of staff, said.

The Hamas leaders had gathered in a private home, in a crowded neighborhood, when the children were out of school. A massive strike would mean civilian casualties. “We had to decide if we’re going to take them out or not,” General Halutz said, adding that he supervised between 80 and 100 targeted killings as head of the air force, “with a 90% success rate.”

In Israel, targeted killing has become a select weapon. In Lebanon last month, Israel targeted a bunker that officials believed held Hezbollah’s leadership, pounding it with 23 tons of explosives. The hit list in Gaza, General Halutz said in an interview, consists of 15 names.

“It is the most important, the most important, method of fighting terror,” General Halutz said.

Most important or not, it is arguably the most morally complicated. Since the beginning of 2006, Israel has targeted and killed 18 Palestinian Arab fighters, according to B’Tselem, an Israeli human rights organization. Fifteen civilians were also killed, the group said.

“We face a tragic dilemma,” Major General Amos Yadlin, chief of military intelligence, said. “A terrorist is going to enter a restaurant and blow up 20 people. But if we blow up his car, three innocent people in the car will die. How do we explain it to ourselves?”

One morning in 2002, General Yadlin recalled, he “woke up horrified” to learn that 15 Palestinian Arab civilians had been killed in an operation. That afternoon, General Yadlin called Asa Kasher, a philosophy professor, and began working on ethical guidelines for fighting terrorism. They also asked a mathematician to write a formula to determine acceptable civilian casualties a dead terrorist.

On September 6, a year later, when Israel had the chance to destroy the Hamas leadership, security officials clashed profoundly over the algebra of assassination. Two officials who have been called Israel’s leaders in combating terrorism took opposite sides. The then head of Shin Bet, Israel’s internal security agency, Avi Dichter, pushed for an all-out assault against the Hamas gathering. “They’re the terrorist dream team,” Mr. Dichter argued.

But for General Yaalon, military chief of staff between 2002 and 2005, the Talmudic precept, “If he comes to kill you, kill him first,” conflicted with a Biblical commandment, “Thou shall not kill.”

Three years later, the men — much like the society from which they come — are still engaged in debate. “It’s still open between us,” Mr. Dichter said, throwing a scolding look at General Yaalon, during a December 2005 forum at the Washington Institute for Near East Policy. “This isn’t settled.”

Afterward, in an interview, General Yaalon looked out the window and said with a sigh: “There are no good answers.”

As chief of staff, General Yaalon carried a pad called “the notebook.” Targets were drawn from the pool of names in the pad, a number that ranged between 300 and 1,000 wanted men, he said. Every militant group is color-coded — red, black, green. When a target was hit, General Yaalon drew an X across his page.

“It’s the lives of Israelis on one hand, the lives of Palestinians on the other,” General Yaalon said, balancing his palms like the scales of justice. He is a tall, balding man, with sloping shoulders, thick glasses, and a taste for meditative poetry. As a youth, General Yaalon joined the leftist kibbutz movement. Despite decades of fighting, he still seems startled by its viciousness.

“When I sign the orders,” he said, “my hand trembles.”

In 2006, despite improved technology, civilian casualties in Gaza have risen. A government spokesman, David Siegel, said the air force launched three times as many targeted attacks in the first eight months of 2006 as it had in all of 2005, increasing the probability of mistakes.

On September 6, 2003, Mofaz’s military secretary, Brigadier General Michael Herzog, was phoning in reports to the defense minister.

“We did it — a direct hit,” General Herzog told him.

A minute later, General Herzog called again: “The results are unclear.”

A minute later: “It seems people escaped alive.”

Another “Whoa!” filled the war room, one of disappointment.

Mr. Dichter recalled: “We saw people running out of the house faster than Olympic runners.”

For Abu Ras, the Hamas leader whose home had been bombed, “it felt like an earthquake. A big, black smoke,” he said in an interview. His guests had sat down to lunch. “I was so happy to host them,” Abu Ras said. “What was our crime? I’m an ordinary citizen, not a terrorist. We have no terrorists among the Palestinian people.”

Palestinian Prime Minister Haniyeh was serving rice to Sheik Ahmed Yassin. Then an explosion shook the room, and Sheik Yassin looked at the ceiling.”Why all this dust? Where is it coming from?” Sheik Yassin, who was lightly wounded in his hand along with another Hamas member and 12 neighbors, said.

Mr. Haniyeh laughed bitterly, “We are hit, Sheik.”

But the men were gathered on the ground floor of the house. The quarter-ton bomb destroyed only the third floor. Abu Ras’s wife and four children, on the second floor, survived. And the Hamas leadership was safe.

The night of the failed operation, General Yaalon sat with his wife watching the news, drinking mint tea. “We didn’t talk about it. It was a very bad weekend,” he said.”Until today, I’m not sure if I was right. I thought about it again, and again, and again. All day long.”