JERUSALEM — Hamas, the militant group that runs the Gaza Strip, has been trying for over a year to keep a lid on its conflict with Israel, to improve the abysmal quality of life for the two million Palestinians under its control, and to keep millions of dollars in cash coming in each month from its generous allies in Qatar.

But a nettlesome, unruly and heavily armed little group called Palestinian Islamic Jihad has repeatedly sabotaged those plans by firing rockets at Israel, which more often than not has responded by raining down destruction on Hamas’s own installations and men.

On Tuesday, impatient with Hamas’s failure to curtail the group, Israel assassinated a top Islamic Jihad commander, a maverick said to be responsible for nearly every instance in the past year in which an incipient cease-fire on the Gaza-Israeli border was wrecked by violence from the Palestinian side.

The killing put Hamas in the uncomfortable position of sitting on the sidelines while its much smaller but more militant rival exchanged blows with their shared hated enemy over two long days of battle.

With Islamic Jihad firing hundreds of rockets into Israel, and Israel answering by killing as many as 20 militants, along with several civilians, Hamas was left to watch the funeral processions roll by and ponder a difficult choice between two roles it has awkwardly balanced for over a decade: Redouble its efforts to achieve quiet along the border? Or revert to its long history as the champion of armed resistance to Israel, and get into the fight?

“By the hour, Hamas gains more criticism from their base,” said Shimrit Meir, an Israeli analyst of the Arab world. “Hamas fighters are watching this and saying, ‘What about us? What have we become?’”

That predicament gets to the heart of the complicated and evolving dynamic between Hamas, the de facto civilian government and 30,000-strong army in Gaza, which has dominated the coastal territory since 2007, and Islamic Jihad, an even older faction that in many ways has been the untrammeled id of the Palestinian resistance movement for some time.

Both groups are viewed as terrorist organizations by Israel and the United States. In times of all-out war, as in 2014, they team up against Israel.

But with Hamas firmly entrenched in Gaza — and Israel preferring to let things stay that way rather than see Gaza and the West Bank reunited — Islamic Jihad has increasingly taken on the role of the ideological purist agitating for violent conflict with Israel, not compromise.

As Gaza’s ruler, by contrast, Hamas is responsible — like it or not — for keeping the peace, a twist from its past role.

In its early years, when Yasir Arafat’s Fatah movement was the dominant Palestinian power in Gaza, Hamas itself played the same sort of tormentor’s role, attacking Israeli soldiers and civilians and making itself look fierce compared to Fatah, which, through the Palestinian Authority, sought to achieve a negotiated settlement with Israel. Back then, Israel would often punish the authority for Hamas’s actions.

Even today, while Hamas ridicules the Palestinian Authority for its security cooperation with Israel on the West Bank, Islamic Jihad’s roughly 6,000 militants often accuse Hamas of doing much the same thing. Hamas, which is largely held responsible by Gaza residents for the awful conditions there, has been seeking a long-term cease-fire with Israel to ease the Israeli-Egyptian blockade and rebuild Gaza’s economy.

Late Wednesday night, it was Islamic Jihad, for a change, that broached a cease-fire: In a televised interview, Ziyad al-Nakhalah, the group’s Lebanon-based leader, said he was waiting for Israel to respond to his terms, which included swearing off future assassinations and stopping the use of live ammunition against Palestinian protesters along the Gaza border fence.

But there was no immediate Israeli response, and in the hour afterward, rockets were fired from Gaza at the cities of Ashdod and Sderot and toward central Israel. And Israel’s military disclosed a new round of airstrikes.

Tensions between Hamas and Islamic Jihad go back decades.

Both groups spun off from the Muslim Brotherhood: Islamic Jihad was founded in 1979 by Fathi Shikaki, a Palestinian inspired by the Shiite Islamic revolution in Iran.

Tareq Baconi, a Gaza expert for the International Crisis Group, said that while the Brotherhood believed Muslims needed to build a “virtuous society before you begin resisting,” Islamic Jihad believed that resistance to the Israeli occupation needed to come first.

When Hamas came into being during the First Intifada, in 1987, it immediately dwarfed Islamic Jihad, said Azzam Tamimi, a Brotherhood-affiliated Palestinian academic and activist based in London.

“Both were initially in competition,” he said. “Islamic Jihad members would say, ‘We didn’t need another resistance movement — we’re already there. You could’ve just supported us.’”

The groups grew closer when Mr. Shikaki was assassinated in Malta, in 1995, and Ramadan Abdullah Shallah, a Gaza-born scholar who had taught Middle Eastern politics at a Florida university, was named Islamic Jihad’s leader.

Mr. Shallah believed the groups should unite into one movement, Mr. Tamimi said. But the Hamas takeover in Gaza led to new friction when some elements of the defeated Fatah movement were merged into Islamic Jihad.

The Syrian civil war created a new divide: Hamas, whose top leaders were in Syria, came out in support of the rebels, rupturing its relationship with Bashar al-Assad’s regime and damaging its ties with Iran. Islamic Jihad did not take sides, and wound up receiving far better funding and weapons deliveries from Tehran, Mr. Baconi said.

Today, while Hamas works with Iran, Israeli analysts say, Islamic Jihad works for Iran: It is considered a full-fledged Iranian proxy, and one that Iran can use to send Israel messages through relatively low-risk acts of violence.

Public opinion may reflect that dual loyalty: While Hamas is supported by about a third of Gaza residents, polls show, Islamic Jihad is the preferred faction of around 5 percent.

Mr. Shallah suffered a series of catastrophic strokes in April 2018, and was replaced by Mr. al-Nakhalah that September. Analysts and Israeli intelligence experts say his hawkishness has made Mr. Shallah look cautious in comparison.

But it was a tactical officer, Baha Abu al-Ata, nominally the commander of Islamic Jihad’s northern brigade, who ordered repeated strikes on Israel in defiance of Hamas’s efforts to achieve a truce along the border, officials and analysts say.

Mediators from Egyptian intelligence, striving along with United Nations officials to broker a cease-fire between Israel and Gaza, brought Mr. al-Ata to Cairo for talks in mid-October.

But within two weeks, Mr. al-Ata was firing rockets into Israel again, officials said.

This week, convinced that Mr. al-Ata was planning a deadlier attack, Israeli officials said, they tracked him down to an apartment in Gaza City. An air-to-ground missile killed him and his wife.

Israel, which has been trying to limit its response to targets associated with the Islamic Jihad, sees the killing as removing a dangerous wild card. That view is likely shared by many leaders of Hamas, analysts suggested.

It is not, at least publicly, shared by Mr. al-Ata’s comrades. “The Israelis said they don’t want escalation, but when you commit such an operation, what does that mean?” said Ihsan Ataya, an Islamic Jihad representative in Lebanon.

If a cease-fire does not take hold, the greater risk for Israelis and Palestinians is that Islamic Jihad’s continued fighting draws Hamas into battle.

“It’s amazing that Hamas is not joining in,” Ms. Meir, the Israeli analyst, said. “It also shows how committed they are to a cease-fire.”

Already, though, she said, Islamic Jihad’s efforts had affected life in Israel.

“They’re very content that they managed to destabilize daily life here,” Ms. Meir said. “I live in Tel Aviv, and my supermarket wasn’t open yesterday. That’s not irrelevant. They have gains on the battlefield.”

Hwaida Saad contributed reporting from Beirut, and Iyad Abuheweilah from Gaza City.

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