Standing on the runway of Dover Air Force Base on Friday, Joe Biden watched solemnly as the flag-draped caskets of three troops were returned to the United States.

Five days earlier, Sgt William Rivers, Specialist Kennedy Sanders, and Specialist Breonna Moffett had been killed in a drone strike in northern Jordan.

As the coffins were unloaded from a military cargo plane and into a van, Mr Biden knew something the families around him did not.

The mission to avenge their fallen relatives had already begun.

Days of planning had gone into the first part of a “multi-tier response” by the US against Iranian-backed militias in Iraq and Syria, inspired by the war in Gaza that began on Oct 7.

On Friday morning, US Air Force B-1B bombers, designed to penetrate Soviet air defences to deliver nuclear bombs, took off from Dyess Air Force Base in Texas for an immense sortie across the Atlantic Ocean to strike more than 85 targets across seven locations in Iraq and Syria.

In a period of just 30 minutes at 9pm GMT, the bombers dropped more than 125 precision munitions on command-and-control centres, rocket and missile stockpiles, drone storage sites and supply chain facilities. Fighter jets and drones already based in the region joined the mission, although there was no involvement from either of the US aircraft carriers in the region.

The list of targets, drawn up by US intelligence officials in the aftermath of the Jan 28 attack in Jordan, included sites used by Iran’s Islamic Revolutionary Guard Corps (IRGC) and an archipelago of loosely allied proxy groups hostile to the US presence in Iraq and Syria.

By 9.10pm, reports had already begun to emerge on social media of a massive bombing raid across the Iraqi-Syrian border.

Footage posted online showed weapons depots ablaze, with rockets and missiles launching uncontrollably in secondary explosions triggered by the US bombs.

The strikes were designed to send a clear message to Iran and its proxies that, although the US presence in Iraq and Syria is relatively small compared to its peak in 2007, the US remains the world’s undisputed military power and can strike its enemies anywhere on the globe.

“The United States does not seek conflict in the Middle East or anywhere else in the world,” Mr Biden said, in a statement released shortly after the attacks had concluded.

“But let all those who might seek to do us harm know this: if you harm an American, we will respond.”

Speaking to reporters on an unusual late night on Friday, Lt Gen Douglas Sims, the Pentagon’s director of operations, said the Biden administration was “pretty confident” about the outcome of the mission in deterring future attacks on US personnel.

“The initial indications were that we hit exactly what we meant to hit,” he said.

John Kirby, the White House’s national security spokesman, said: “We do not know at this time if or how many militants may have been killed or wounded. All US aircraft are now out of harm’s way.”

The US bombers returned to base at the end of a 44-hour, 15,000-mile round trip – the longest bombing raid and most complex aerial assault carried out by the US since the invasion of Iraq in 2003.

The Pentagon has now begun a full battle damage assessment that will estimate the impact of the strikes on Iranian forces and those of the Islamic Resistance in Iraq (IRI), an umbrella grouping of Tehran-backed militants.

Mr Kirby said that the mission had two primary objectives. The first was to send a message to Iran that the militants war of attrition against US bases in the region with suicide drones and missiles would not be tolerated by Washington.

“The signal is, to the IRGC and to these groups: the attacks have got to stop,” he said.

The second objective is to erode the militants’ ability to launch further assaults by destroying the weapons they use.

The White House has been clear for weeks that the US believes Iran is providing weapons and funding for strikes on US forces. IRGC troops are operating alongside the IRI, running military bases and supply lines into Iraq and Syria.

Friday’s bombing run hit a diverse range of targets, including command-and-control centres, intelligence headquarters, storage sites for rockets, missiles and drones, and ammunition supply chain facilities.

Some of those targets were used by the IRGC’s Quds Force – the armed forces’ foreign espionage and paramilitary arm – and some by the IRI groups it operates with, according to the US Centcom.

However, with Washington concerned about the prospect of a full-scale war with Iran, the Pentagon’s unspoken caveat was that the bombs were not designed to kill a large number of troops.

Official numbers are not yet public, but an initial assessment by the Syrian Observatory for Human Rights said that the strikes killed 23 pro-Iranian fighters in Syria, while Baghdad has said they killed 16 people in Iraq, including civilians.

The small death toll – of less than one person killed for every two precision bombs dropped – is a result of the White House’s decision to broadcast its intention to strike in Iraq and Syria for days before the mission began.

By Sunday afternoon, hours after the three US troops were killed in Jordan, Mr Biden was vowing to strike back against those responsible.

Although there was no behind-the-scenes contact between the US administration and Iran between Sunday morning and Friday night, public appearances by US officials had given a strong indication of what the mission would involve.

Tehran recalls its troops

Off-record briefings to US news organisations made clear that the targets would be in Iraq and Syria, not on Iranian soil, and that they would include facilities run by the IRGC.

By Monday, Tehran had already begun to recall its troops stationed in the region, launching evacuations of bases that had been used in attacks against the US. The Iranian regime issued an alarmed statement denying responsibility for the drone strike in Jordan.

Three days later, Lloyd Austin, US defence secretary, gave a Pentagon press briefing describing a “multi-tier response” designed to defend US troops while avoiding war with Iran.

Elsewhere in the same building, administration officials made a decision to hold off on strikes that night because of poor visibility that could endanger civilians near the targets.

The clearly telegraphed warnings to Iran appear to have allowed the IRGC to minimise its losses, and will likely have resulted in the removal of weapons from facilities in Iraq and Syria that Tehran expected to be targeted in the retaliatory strikes.

Although the White House has not discussed its strategy publicly, US officials have been clear that Mr Biden is trying to avoid a full-scale conflict with Iran. Killing a large number of IRGC troops risked inflaming tensions further and worsening the reprisals against US forces.

The strikes nonetheless provoked an immediate response from the Islamic militias.

Within hours, as the B-1B bombers embarked on their 6,000-mile return to Texas, the IRI claimed it had launched a drone strike on the al-Harir air base hosting US forces in northern Iraq, although some security officials suggested the attacks had not been successful.

‘Strategic mistake by US’

On Saturday morning, an Iranian foreign ministry spokesman said the air strikes were “violations of the sovereignty and territorial integrity” of Syria and Iraq and represent “another adventurous and strategic mistake by the United States that will result only in increased tension and instability in the region”.

Iran has also urged the UN Security Council to intervene, to prevent “illegal and unilateral US attacks”, and summoned its US envoy in Tehran, while state television networks described US forces as “terrorists”.

“The root cause of tensions and crises in the Middle East is Israel’s occupation and genocide of Palestinians with America’s unlimited support,” the spokesman said.

An Iraqi government response claimed that the bombings “undermine the efforts of the Iraqi government” and could “lead Iraq and the region into dire consequences”.

Syria’s government in Damascus said that “occupying parts of Syrian lands by American forces cannot continue,” adding: “The Syrian army affirms continuing its war against terrorism until it is eliminated and is determined to liberate the entire Syrian territories from terrorism and occupation.”

Little is known about what the next phase of the US response will be, and it will likely be shaped by the events of the next 48 hours, as Washington assesses the diplomatic and military impact of its strikes.

There is talk of the US launching a cyber attack on Iran or its proxy groups, and it is possible that there could be a second round of air strikes to further damage military targets.

The only option that has been explicitly ruled out is a direct attack on Iranian soil, a move that Washington believes would plunge the US into a full-scale war with Tehran.

On Saturday morning, as he flew to a campaign event from the same air base where he watched US troops brought home on Friday, Mr Biden considered his next steps.