They came dropping from the sky in the dead of night. It was 4.15am local time last Monday, when Israeli navy commandos were lowered from helicopters onto the decks of the six vessels which consisted the so-called freedom flotilla. Surrounding the flotilla were navy vessels. The Israelis were taking it upon themselves to commandeer the vessels in international waters.

The main action was confined to the Turkish ship, the Mavi Marmara. Versions of what occurred differ greatly.

According to the Israelis, the navy men merely defended themselves after coming under attack from firearms and deadly weapons. Those on the ship tell a different story.

Initially, three soldiers landed on the ship and were overpowered. A large number of the passengers were standing on the upper deck, determined to resist the boarding of their vessel by armed men in international waters.

According to Andre Abu-Khalil, a cameraman for Al Jazeera TV, there was no negotiation or interaction with the soldiers who boarded the vessel.

"There were 20 Turkish resistance guys throwing tomatoes, anything that they managed to throw, on the Israelis. Then one of these Turkish guys got a bullet just in the head. When the Turkish guys saw that, they pulled him inside when the Israelis started firing on the deck."

The Israelis took full control of the vessel just over an hour after the first assault. Everybody was taken from their cabins and tied up. Nine people, including eight Turkish nationals, were shot dead, and up to a dozen others injured.

Hazam Farouq, an Egyptian MP and dentist, who was on board, recalled what he saw.

"Four people died before my eyes and in my hands," he said. "We could not find any first aid material. What happened required a field hospital to treat the injured. I did not have the necessary material to treat their bleeding wounds.

"When we tried to carry the injured, the Israeli soldiers refused to allow men to carry the wounded. They pointed their guns with laser light toward their heads. They asked women to carry the wounded. Some women could not."

The weapons subsequently put on display by the Israelis were implements likely to be kept on any large vessel. There were no guns found, despite the contention that the soldiers had come under fire.

All six vessels were set on course for the southern Israeli port of Ashdod. There was minimal resistance to the boarding of the other five vessels.

The flotilla was never going to be allowed through to Gaza. Israel had made that clear. Three days before the flotilla left Cyprus, an Israeli foreign ministry spokesman stated its position. "This is a territory in a self-declared state of war with Israel. There can be no uncontrolled transportation in or out of Gaza."

The organisers, for their part, were aware of the political capital to be garnered from the venture. If the world could see that Israel was preventing humanitarian aid reaching 1.5 million Palestinians, packed like sardines on the strip, it might bring pressure to bear on Israel to lift the blockade.

Israel imposed the blockade in 2007, after Hamas had seized control of the strip. The party had won elections earlier that year, but a power struggle ensued with rival faction Fatah, which was ultimately ejected.

Hamas sanctions regular rocket attacks into Israel and is committed to the destruction of the Jewish state. Israel's response to Hamas rule was to impose a blockade, ostensibly to prevent the import of weapons, but it is widely interpreted as an attempt to turn the wider populace against Hamas. Egypt has also complied with the blockade. There is no sign that the strategy of turning the population against Hamas is working.

The constant rocket attacks led to Israel invading the strip in 2008, sparking off a three-week violent conflict that left much of Gaza in ruins. The reaction was in keeping with the long running theme of the Israeli/Palestinian problem – proportionality. Israel's habitual reaction to attacks, and seeming disregard for civilian casualties, suggests it regards one Israeli life as being equivalent to dozens, if not hundreds, of Palestinian lives.

Some ships have been allowed through to Gaza, but others blocked irrespective of their cargo. This flotilla was of a different scale to anything attempted before.

Two main organisers were behind the effort. The Free Gaza Movement was established in September 2006 by a group of Palestinian supporters. It is based in Cyprus, with branches in many countries, including Ireland. Its founder, 69-year-old Greta Berlin, says she was married to a Palestinian for 14 years, and to an American Jew for another 14. She is currently single.

"We asked ourselves what can we do to make a difference?" she said last week. "We said, 'let's sail a boat to Gaza'. That was literally how it started."

Three attempts to land aid over the last few years ended in failure. The difference this time was the inclusion of the other flotilla organiser, a Turkish charity, Insani Tardim Vakfi, known by its Turkish initials, IHH.

The group was founded as a charity for the poor in Istanbul, and later for Bosnian war victims. It draws its support from the Muslim business class in Turkey, which accounts for the majority of donations. It is now involved in relief work in dozens of countries.

Israel claims IHH has links with Hamas, which IHH denies. Israel's animosity towards IHH has added to a loosening of close relations between the Jewish state and Turkey, which has a large Muslim population. Those relations took another dive on Monday.

Among the sanctions imposed on Gaza by Israel is a 23-mile sea exclusion zone. The sanction has had a devastating effect on fishing, the only natural resource to which Gazans have access. There was always going to be trouble once the flotilla entered the exclusion zone. As it was, the Israel Defence Forces (IDF) decided to act in international waters, boarding ships in a manner that has drawn comparisons with piracy.

Reaction to the violent deaths followed the same pattern that has been established over the past 40 years. Angry demonstrations formed outside Israeli embassies across the world. The UN Security Council called an emergency meeting. All eyes were on the USA. Barack Obama's response said it all. He expressed "deep regret" over the incident.

He didn't condemn the killings of apparently unarmed civilians. He didn't even call into question the legal or moral right to commandeer vessels in international waters. He made no mention of the issue at the heart of the matter – a blockade that is a humanitarian disaster. Deep regret was as far as he went.

Obama's words were in contrast to those of Turkey's prime minister, Recep Tayyip Erdogan. He called the attack "a bloody massacre" and called for an end to "the inhumane embargo on Gaza".

In New York, the UN Security Council went into emergency session. The USA's influence was brought to bear on the statement that followed. The 15-member council "deeply regrets the loss of life and injuries resulting from the use of force during the Israeli military operation in international waters against the convoy sailing to Gaza".

As the world condemned the attack, the exemplary Israeli PR machine went into overdrive. There was a news blackout from the detained activists, enabling the IDF to gets its version of events out first. The soldiers claimed they had opened fire after coming under attack. Army footage was released purporting to show attacks on the military personnel.

An allegation – never substantiated – was thrown out that some of the activists produced firearms. In Canada, Israeli prime minister Benjamin Netanyahu regretted the loss of life but claimed the navy commandos were "mobbed, clubbed, beaten and stabbed".

Yet, despite the bravado, questions were being raised even in Israel about how its strategic interests had been damaged by the heavy-handed approach.

Meanwhile, as the diplomatic lines burned and sizzled, back in the real world, the killing and dying continued. Two gunmen identified as members of Islamic Jihad were killed by Israeli troops after crossing the border from Gaza. Later in the day, the Israeli airforce killed three militants in northern Gaza who were preparing to fire rockets across the border, the latest in the daily indiscriminate attacks that are launched on Israeli towns.

Down in the port of Ashdod, the flotilla arrived under heavy guard. Up to 600 activists were detained. Irishman Shane Dillon would later describe how he was manhandled by military personnel when he refused to hand over his passport. Fintan Lane later described how soldiers photographed and sneered at the activists, who had effectively been kidnapped. In total, seven Irish passport-holders were among those detained.

Out on the Mediterranean, the MV Rachel Corrie was two days out of port, steaming towards Gaza. Technical difficulties had kept it behind the main flotilla. Now it was on the way. Crewed by Irish and Malaysian personnel, it was carrying 1,200 tonnes of supplies and it was intent on breaking the blockade.

The Irish-owned ship was named after an American aid worker who was crushed to death in Gaza in 2003 by an IDF bulldozer that was flattening a Palestinian home.

On Wednesday, the captured activists were processed, transferred north to Tel Aviv and put on planes bound for Turkey. The nine coffins, eight of them containing Turkish nationals, were also placed on one of the planes.

Netanyahu gave a televised bullish address to the nation, defending the navy's actions and accusing the international community of hypocrisy. His defence minister echoed these thoughts when thanking the commandos in a visit to their base.

"We need to always remember that we aren't North America or western Europe. We live in the Middle East, in a place where there is no mercy for the weak and there aren't second chances for those who don't defend themselves," he said. The words might just as easily have been spoken by a Palestinian leader in reference to their plight.

In Ireland, the Israeli ambassador Zion Evrony reneged on a pledge to appear before an Oireachtas committee on Thursday to explain his country's actions. It would appear that the PR strategy had shifted from trotting out the standard line to saying nothing at all.

Foreign affairs minister Micheál Martin issued a warning about any interference with the Rachel Corrie. "It has been a terrible week in terms of the loss of life and there is now an obligation on all involved to reduce tensions… It is extremely important that we do not have a repeat of what happened earlier this week."

The progress of the Rachel Corrie was being tracked across the airwaves in Ireland, with a satellite phone link with the vessel. Denis Halliday, the former UN assistant secretary-general, said the crew of 15 were determined to deliver their cargo.

"We are the only Gaza-bound aid ship left out here," he said. "We are determined to deliver our cargo, which includes 1,000 tonnes of cement and 20 tonnes of educational materials and toys, along with vital medical supplies."

Cement is among the list of banned materials on the basis that it could be used by Hamas to build tunnels from which to launch attacks on Israel.

Thursday dawned with a huge outpouring of grief in Turkey as the funerals of the slain activists began. Islamic funerals involve explicit expressions of grief, and these are naturally accompanied by serious expressions of hatred for those deemed responsible for the deaths. It's a scene that is familiar in Middle Eastern countries, but now Turkey – heretofore a relatively close ally of Israel – has quickly changed direction.

Word seeped out in Ireland that there were more woes for Israel on the diplomatic front. An official from the Israeli embassy is reportedly due to be expelled over the use of fake Irish passports in the Israeli assassination of a Hamas figure in a Dubai hotel earlier this year.

In the US there were indications that Israel will have to change its policy on the blockade. One government official told the New York Times: "There is no question that we need a new approach to Gaza… Gaza has become a symbol in the Arab world of the Israeli treatment of Palestinians and we need to change that," he said.

Later, Obama confirmed the administration's thinking in an interview on CNN: "I think what's important right now is that we break out of the current impasse, use this tragedy as an opportunity," he told Larry King. It was the first indication that the flotilla might not have sailed in vain, despite the heavy price that had been paid in loss of life.

By Friday, change was floating on the wind. The Israeli cabinet was examining proposals to ease the blockade, in response to pressure both internally and from the USA. The proposal involves international inspectors searching ships bound for the strip to ensure that no weapons are aboard. The inspections would take place at the port of Ashdod, or some other strategic location. If all was okay, the vessels would then be allowed onward to Gaza. The change would ease some of the suffering among Gazans, 80% of whom now have to queue for food every day.

Meanwhile in Iran, supreme leader Ayatollah Ali Khamenei used the Friday prayers to hit out at the massacre and said Israel was approaching its death "step by step". The intolerance and hatred displayed by the religious leader of Israel's principal enemy in the region was the only real positive PR that the Jewish state had all week.

Out on the Mediterranean, the Rachel Corrie inched closer to Gaza and interception. Yesterday it was boarded by the IDF, but by then it had served its purpose, keeping the issue of the blockade current through the days of diplomatic wrangling. At the end of a week that began violently, there is at least a slight prospect that the appalling conditions on the Gaza Strip might be somewhat alleviated. That it took the deaths of nine people to achieve it speaks volumes for the nature of a conflict that shows no signs of abating.