The Israel Defense Forces had little trouble explaining the naval commando raid yesterday to the Israeli public. The troops slid from helicopters into a violent crowd, which attacked them with sticks. It's no wonder the troops opened fire in self-defense.

The situation in the international arena, though, is the diametric opposite. No matter how much effort it invests, Israel will never be able to explain to the world how nine civilians were killed, without a single death on our side - and the dead are citizens of the country that was until recently our best friend in the region. The consequences of this incident will necessitate a far-reaching investigation of the decision-making process and the execution.

Israeli spokesmen repeatedly stressed yesterday that the demonstrators went into a violent frenzy that endangered the soldiers' lives. This argument, however, should not detract attention from the question of why these things happened, and whether an alternative had been possible. Ultimately, Israel walked straight into the trap that the flotilla organizers set, and has found itself in a massive diplomatic mess. It remains unclear what Israel should do about the next aid ship, which is due to set sail for Gaza today or tomorrow.

One of the most telling images of the day, along with footage from the ships, was the expression of Navy Commander Major General Marom at the noon press conference. The many weeks the navy spent preparing to meet the flotilla, the advance praise it received for its professional preparations, all culminated in a resounding failure. We should be clear: If Israel's goal was to "contain" the flotilla and prevent it from triggering a major crisis, we failed utterly and completely, and in no way is this the soldiers' fault.

Before we address the army's part in the fiasco, we would need to meticulously investigate the political leadership's conduct. Israel's siege on Gaza began soon after Hamas' 2006 election victory, and intensified after Gilad Shalit was abducted and Hamas ousted Fatah from power a year later. The siege has had limited success at best. Hamas may be fairly isolated, but the weapon smuggling has continued, and the blockade has done nothing to advance Shalit's cause.

Another question concerns the enforcement of the blockade. The Olmert government had allowed aid ships to assist the Gazans. The current government blocked an aid ship a year ago, effectively and without casualties. The decision on this morning's operation was made unanimously by the seven-member security cabinet. Israel left itself having to decide, at the latest possible moment, between two unenviable alternatives: taking over the ships, or allowing the flotilla to pass, unimpeded and unexpected, into Gaza. The critical juncture may actually have been earlier: changing the fruitless siege policy, or taking less blatant steps against the flotilla, such as damaging their engines or physically blocking their path, without sending combat soldiers to board them.

As for the operation itself, the commandos did nothing wrong. They were vastly outnumbered, and apparently prepared only for a disturbance, with limited use of cold weapons. When they descended from their ropes onto the decks, they found themselves amid a violent mob. Sliding down a cable is done wearing asbestos gloves, which make it impossible to operate a weapon. Some soldiers were armed only with paintball rifles.

While they wrestled with the protesters, at least two pistols were snatched from them. The outnumbered commandos were at risk of having their comrades lynched, and opened fire. A Turkish policeman or soldier would not have shown any more restraint. The result, at any rate, was horrific: Civilians were killed, and the protesters threw a commando from the upper deck to lower deck. It's not just appalling footage, it's a national humiliation and a blow to Israeli deterrence. The question is why the soldiers were put into this situation in the first place.

The IDF had all the time in the world to prepare for the flotilla. The entire intelligence community had all the time it needed to follow the protesters' plans and preparation. Drones provided constant streaming videos of the ships, and it's safe to assume other means of tracing and sabotage were used: Signal jamming, signal tapping, possibly even live agents. And still, based on the commandos' testimonies yesterday, it's clear they were not prepared for what awaited them on the deck. The IDF underestimated the resistance the protesters would show, and possibly their numbers as well.

But neither should the intelligence community shoulder all of the blame. Everyone in the top brass, from the defense minister to the chief of staff and down, confirmed the plan. "We were arrogant and complacent," one officer told Haaretz. "We didn't anticipate the scale of the resistance and didn't conduct ourselves accordingly."

Moreover, the force lacked the element of surprise, as protesters knew an assault was imminent. We also know by this stage that a critical mass of soldiers did not board the Marmara early enough, and it may be that not enough troops were allocated to begin with. The end result remains the same: The commandos were not prepared to confront such a large, violent crowd.

The choice of unit for the operation was criticized yesterday, as small-scale ego wrestling began between elite units and their commanders; the Shayetet's specialty is not crowds, but enemy combatants. But it seems the elite naval commando unit was chosen because of the challenge the IDF faced - taking control of a moving vessel, a feat considerably more difficult than it appears to be on TV.

Whatever way one looks at it, the end result is bad, especially for Israel. The repercussions go far beyond the question of which unit was sent on the mission. Ankara withdrew its ambassador from Tel Aviv, and it may well come to an end to relations; prospects of tourism and military cooperation don't appear particularly solid anymore. The Erdogan government is far from innocent, of course - it supported the flotilla, and has been inflaming the public against Israel in Turkey for a while.

Closer to home, persistent but unfounded rumors that Sheikh Ra'ad Salah had been killed on one of the ships could have started public unrest much like the infamous October 2000 riots. There does not appear to be a conflagration arising in the territories, as Palestinians in the West Bank remain critical of Israel but don't rush to confrontation.

Hamas is bound to use the entire affair for its needs, and to try and ease the siege. Europe has been ripe for such a move for a while, and it remains to be seen whether the Obama administration will try to pressure Netanyahu. Either way, the Israeli failure to address a provocation by Islamist activists and radical leftists is now a strategic one.