Iran-Pakistan Flare-up Rooted in Restive Borderlands, Not Mideast Strife

The flag of Iran is seen over its consulate building, with Pakistan's flag in the foreground, after the Pakistani foreign ministry said the country conducted strikes inside Iran targeting separatist militants, two days after Tehran said it attacked Israel-linked militant bases inside Pakistani territory, in Karachi, Pakistan January 18, 2024. REUTERS/Akhtar Soomro
The flag of Iran is seen over its consulate building, with Pakistan's flag in the foreground, after the Pakistani foreign ministry said the country conducted strikes inside Iran targeting separatist militants, two days after Tehran said it attacked Israel-linked militant bases inside Pakistani territory, in Karachi, Pakistan January 18, 2024. REUTERS/Akhtar Soomro
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Iran-Pakistan Flare-up Rooted in Restive Borderlands, Not Mideast Strife

The flag of Iran is seen over its consulate building, with Pakistan's flag in the foreground, after the Pakistani foreign ministry said the country conducted strikes inside Iran targeting separatist militants, two days after Tehran said it attacked Israel-linked militant bases inside Pakistani territory, in Karachi, Pakistan January 18, 2024. REUTERS/Akhtar Soomro
The flag of Iran is seen over its consulate building, with Pakistan's flag in the foreground, after the Pakistani foreign ministry said the country conducted strikes inside Iran targeting separatist militants, two days after Tehran said it attacked Israel-linked militant bases inside Pakistani territory, in Karachi, Pakistan January 18, 2024. REUTERS/Akhtar Soomro

An Iranian strike on Pakistan this week that drew a rapid military riposte and raised fears of greater regional turmoil was driven by Iran's efforts to reinforce its internal security rather than its ambitions for the Middle East, according to three Iranian officials, one Iranian insider and an analyst.
Both the heavily-armed neighbors, oftentimes at odds over instability on their frontier, appear to want to try to contain the strains resulting from the highest-profile cross-border intrusions in recent years, two analysts and two of the officials said.
Iran sent shockwaves around the region on Tuesday with a missile strike against what it described as hardline “Sunni Muslim militants” in southwest Pakistan. Two days later, Pakistan in retaliation attacked what it said were separatist militants in Iran - the first air strike on Iranian soil since the 1980-88 Iran-Iraq war.
Tuesday's strike was one of Iran's toughest cross-border assaults on the militant Jaish al-Adl group in Pakistan, which it says has links to ISIS. Many of Jaish's members previously belonged to a now-defunct militant group known as Jundallah that had pledged allegiance to ISIS.
The move deepened worries about Middle East instability that have spread since the Israel-Hamas war erupted in October. Iran-allied militias from Yemen to Lebanon have launched strikes on US and Israeli targets, including on Red Sea shipping, in sympathy with Gaza's Palestinians.
It also came a day after Iran launched attacks in Iraq and Syria, which it said targeted Israeli espionage and ISIS operations, respectively.
But the tit-for-tat blows between Iran and Pakistan occurred far from that war zone, in remote borderlands where separatist groups and Islamist militants have long carried out attacks on government targets, with officials in Pakistan and Iran often accusing each other of complicity in the bloodshed.
Gregory Brew, an analyst at Eurasia Group, an international risk consultancy, said Tehran's strikes were motivated in large part by Iran's rising concerns about the threat of domestic militant violence in the wake of a deadly Jan. 3 bombing claimed by the ISIS group.
"There's a lot of domestic pressure to 'do something,' and the leadership is responding to that pressure," he said.
Spokespeople for the Iranian and Pakistani foreign ministries could not immediately be reached for comment.
'CRUSHING RESPONSE'
Pakistan recalled its ambassador from Iran in protest at Tuesday's attack. For its part, Tehran strongly condemned Pakistan's strikes on Thursday, saying civilians were killed, and summoned Pakistan's most senior diplomat in Iran to give an explanation.
But in their statements, neither government sought to make a link to the Gaza war or to attacks carried out in support of Palestinians by a network of militias allied to Iran.
In a public statement on Thursday, the foreign ministry in Tehran said: "Iran considers the security of its people and its territorial integrity as a red line" and expects "friendly and brotherly" Pakistan to prevent armed militant bases on its soil.
For Iran, the trigger for the flare-up was a devastating bombing on Jan. 3 that killed nearly 100 people at a ceremony in the southeastern city of Kerman to commemorate commander Qassem Soleimani, who was killed by a US drone in 2020.
Soleimani, architect of Iran's drive to extend its influence across the Middle East, was a hero to supporters of the hardline establishment. Tehran publicly vowed revenge against ISIS militant group that claimed responsibility for the bombing.
An Iranian insider close to the country's ruling clerics described the Kerman bombing as "an embarrassment for the leadership" that had shown Iranian security to be vulnerable.
Tuesday's strike was aimed at demonstrating the security organizations' capabilities amid concern among Iranians about a lack of security in the country, the Iranian insider said.
"Such terrorist attacks will get a crushing response from Iran," the insider said.
Iran has also arrested dozens of people linked to ISIS.
On Tuesday, Iranian missiles struck two bases of the Jaish al-Adl (or the Army of Justice) group in Pakistan's southwestern province of Balochistan, which borders Iran.
A senior Iranian security official told Reuters that Iran had provided Pakistan with evidence that Jaish al-Adl was involved in the Kerman attack, coordinating its logistics, and had asked Pakistan to act against it. Iran had obtained evidence that members of the group were among a number of militants planning further attacks in Iran, he said.
"We have warned everyone that any action against our nation, our national security will not go unanswered," the official added, speaking on condition of anonymity due to the sensitivity of the matter.
IRAN 'LOST PATIENCE'
Iran has been pressing Islamabad for years to address the presence of militants near its border, Brew said. The missile strikes were a sign that Tehran has lost patience, he said.
To be sure, Iran continues to see its role and influence in the Middle East as a central to its security goals.
Brew said that Iran's strike on Pakistan was also intended to signal its resolve, to both enemies and allies, to defend itself in the context of the regional crisis over Gaza.
Michael Kugelman, director of the South Asia Institute at the Wilson Center, a Washington-based think tank, said bilateral tension on border security was a longstanding problem for Iran and Pakistan.
De-escalation would be difficult in the immediate term, "given the high tensions and temperatures at play", he said.
Neither country appears poised for conflict, however. In public statements, both countries have observed their attacks were not aimed at each other's nationals, and signaled they don't want escalation.
Kugelman said both countries might welcome bilateral dialogue and potential third party mediation from a country like China, which has good relations and leverage with both countries. "Diplomacy will be critical from here on out," he said.



A Week Into the Fragile Israel-Iran Peace Agreement, Here's What We Still Don't Know

People attend the funeral procession of Iranian military commanders, nuclear scientists and others killed in Israeli strikes, in Tehran, Iran, June 28, 2025. Majid Asgaripour/WANA (West Asia News Agency) via REUTERS
People attend the funeral procession of Iranian military commanders, nuclear scientists and others killed in Israeli strikes, in Tehran, Iran, June 28, 2025. Majid Asgaripour/WANA (West Asia News Agency) via REUTERS
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A Week Into the Fragile Israel-Iran Peace Agreement, Here's What We Still Don't Know

People attend the funeral procession of Iranian military commanders, nuclear scientists and others killed in Israeli strikes, in Tehran, Iran, June 28, 2025. Majid Asgaripour/WANA (West Asia News Agency) via REUTERS
People attend the funeral procession of Iranian military commanders, nuclear scientists and others killed in Israeli strikes, in Tehran, Iran, June 28, 2025. Majid Asgaripour/WANA (West Asia News Agency) via REUTERS

It's been a week since the United States pressed Israel and Iran into a truce, ending a bloody, 12-day conflict that had set the Middle East and globe on edge.

The fragile peace, brokered by the US the day after it dropped 30,000-pound "bunker-busting" bombs on three of Iran's key nuclear sites, is holding. But much remains unsettled, The Associated Press reported.

How badly Iran’s nuclear program was set back remains murky. The prospects of renewed US-Iran peace talks are up in the air. And whether US President Donald Trump can leverage the moment to get Israeli Prime Minister Benjamin Netanyahu 's government and Hamas focused on a ceasefire and hostage deal that brings about an end to the 20-month war in Gaza remains an open question.

Here is a look at what we still don't know:

How far Iran's nuclear program has been set back Trump says three targets hit by American strikes were “obliterated.” His defense secretary said they were “destroyed.”

A preliminary report issued by the US Defense Intelligence Agency, meanwhile, said the strikes did significant damage to the Fordo, Natanz and Isfahan sites, but did not totally destroy the facilities.

Rafael Grossi, head of the International Atomic Energy Agency, said on CBS’ “Face the Nation” on Sunday that the three Iranian sites with “capabilities in terms of treatment, conversion and enrichment of uranium have been destroyed to an important degree.” But, he added, “some is still standing” and that because capabilities remain, “if they so wish, they will be able to start doing this again.” He said assessing the full damage comes down to Iran allowing inspectors access.

What future US-Iran relations might look like

After the ceasefire deal came together, Trump spoke of potentially easing decades of biting sanctions on Tehran and predicted that Iran could become a “great trading nation” if it pulled back once-and-for-all from its nuclear program.

The talk of harmony didn't last long.

Ali Khamenei, in his first public appearance after the ceasefire was announced, claimed Tehran had delivered a “slap to America’s face." Trump responded by suggesting the supreme leader own up to the fact Iran “got beat to hell. The president also said he was backing off reviewing any immediate sanction relief, because of Khamenei's heated comments.

White House officials say the US and Iran are already in early discussions about resuming negotiations that had ended after Israel began launching strikes. But Iranian Foreign Minister Abbas Araghchi says there's no agreement in place to restart talks.

It's unclear if Iran's leadership is ready to come to the table so soon after the fighting has ended — especially if Trump holds to the position that Iran must give up nuclear enrichment for even civilian use. And Trump has offered conflicting statements about his commitment to talks. “We may sign an agreement,” he said Wednesday at a NATO summit press conference. He added, “I don’t think it’s that necessary.”

What role Iran's supreme leader will play

Khamenei's age and recent diminished appearance have raised questions about the scope of his involvement in US-Iran relations and Iran's response to both American and Israeli strikes. But despite having spent the last few weeks in a bunker as threats to his life escalated, there is little indication that Khamenei does not still reign supreme over the country's massive military and governmental operations.

Khamenei has ruled three times longer than his predecessor, the late Ruhollah Khomeini, and has shaped life for the country's more than 90 million people perhaps even more dramatically.

He entrenched the system of rule by the “mullahs,” or Shiite Muslim clerics. That secured his place in the eyes of hard-liners as the unquestionable authority, below only that of God. At the same time, Khamenei built the paramilitary Revolutionary Guard into the dominant force in Iran’s military and internal politics.

How Iran might strike back Iran's retaliatory missile attacks on a US base in Qatar following the American bombardment were sloughed off by the White House as a half-hearted, face-saving measure. The US was forewarned and the salvos were easily fended off.

Yet Iran remains a persistent threat, particularly via cyberwarfare. Hackers backing Tehran have already targeted US banks, defense contractors and oil industry companies — but so far have not caused widespread disruptions to critical infrastructure or the economy.

The US Department of Homeland Security last week issued a public bulletin warning of increased Iranian cyber threats. And the US Cybersecurity and Infrastructure Security Agency, is urging organizations that operate critical infrastructure like water systems, pipelines or power plants to stay vigilant.

Whether the Israel-Iran ceasefire will hold It remains a fragile peace.

Immediately following the US strikes, Trump got on the phone with Netanyahu and told the Israeli leader not to expect further US offensive military action, according to a senior White House official who was not authorized to comment publicly about the sensitive diplomatic talks.

But even as he agreed to deal, Netanyahu made clear that Israel will strike again “if anyone in Iran tries to revive this project.”

The ceasefire deal came without any agreement from Tehran on dismantling its nuclear program. Khamenei claims the attacks “did nothing significant” to Iran's nuclear facilities.

Trump expressed confidence that Iran, at the moment, has no interest in getting its nuclear program back up. “The last thing they’re thinking about right now is enriched uranium,” Trump said.

Still, Trump says he expects Iran to open itself to international inspection to verify that it doesn’t restart its nuclear program by the International Atomic Energy Agency, the UN nuclear watchdog, or some other organization "that we respect, including ourselves.”

Whether Trump can now press Netanyahu on Gaza

The president took a big gamble with his decision to order strikes on Iran's nuclear fortress.

As a candidate, he promised to quickly end Russia's brutal war in Ukraine and the Israel-Hamas conflict in Gaza, but has failed to find a resolution to either. He also vowed to keep the US military out of foreign conflicts.

But after helping Israel with US strikes on Iran, Trump — in conversations with Netanyahu and other world leaders in recent days — has made clear he wants a deal completed soon, according to two people familiar with the private discussions and were not authorized to comment publicly.

On Friday, Trump told reporters, “We think within the next week we’re going to get a ceasefire.”

Trump didn't offer any further explanation for his optimism. But Israeli Minister for Strategic Affairs Ron Dermer is expected to be in Washington this week for talks on a Gaza ceasefire, Iran and other matters, according to an official familiar with the matter. The official spoke on condition of anonymity because they were not authorized to speak to the media.