The raid has sparked protests across the world
There is widespread agreement in Israel and around the world that, whatever the rights or wrongs about the Gaza flotilla, something went badly wrong with the operation to stop it.
One commentator in the Israeli newspaper Haaretz remarked that "my six-year-old son could do much better than our current government."
So, what went wrong?
The interception took place about 40 miles (60km) off the Gaza coast, some 25 miles beyond the formal limits of the maritime blockade Israel is maintaining on Gaza.
A maritime blockade is a legal device under international law. It has to have a reason (Israel's is that Hamas would import arms), it has to be formally declared (it was) and it has to be enforced (it is).
By intercepting beyond the blockade limits, Israel took a risk that the action would be challenged under international law, but the issue is at least debatable.
Israel argues that the flotilla clearly intended to try to run the blockade, and indeed the lead ship said its destination was Gaza when told to stop over a radio channel by the Israelis in the formalities at the start of the action.
Five of the six ships in the flotilla did stop, but the main one, the Mavi Marmara, did not.
(Update: several readers have pointed out that the protesters, as well as the UN high commissioner for human rights, consider the whole blockade illegal and that therefore, in their view, the Israeli argument becomes irrelevant.)
Warnings having predictably failed, Israel decided to use force.
It did so using members of its seaborne special forces, Flotilla 13, with helicopters and speed boats.
There has been debate within Israel as to whether this was the right unit to use. It is trained for combat, not crowd control.
The best account so far of what happened has come from Ron Ben Yishai, a reporter with the Israeli newspaper Yediot Achronot, who was an eyewitness.
Israeli army footage showing the violence on board the flotilla - the captions and circled points on this video were inserted by the Israeli army
He says the plan was to land a team on the top deck and rush the bridge and take control. The assessment, he reports, was that the passengers would show "light resistance and possibly minor violence".
The soldiers, he says, were told to confront protesters verbally, use crowd control tactics and use firearms only to save their own lives.
However, as the first troops rappelled down, one by one, "the unexpected occurred. The passengers... pulled out bats, clubs and slingshots with glass marbles, assaulting each soldier as he disembarked".
You can see some of this on a video taken by the Israelis. Individual soldiers landing on deck are outnumbered and set upon. One protester using a club is wearing a gas mask. Other videos released by the Israelis show the catapults, marbles, metal rods and a knife they recovered.
Ron Ben Yishai mentions the bizarre use by the soldiers of paintball guns. You can see one of them in profile on the video. These, he said, were not effective. One wonders whether paint was actually in them or some other substance, but in any case they did not work
Ron Ben Yishai Israeli reporter
The unexpected occurred. The passengers... pulled out bats, cubs and slingshots with glass marbles, assaulting each soldier as he disembarked
The commandos were unable to rush the bridge as planned and a second troop was sent in from another helicopter. By now about 30 activists were confronting about 30 troops on deck.
But something more serious was happening. The reporter states that the protesters "attempted to wrest away [the soldiers'] weapons". They got hold of one handgun, he says, when one soldier, seen on the video, was thrown from the upper deck on to the lower.
(Update: this soldier has now identifed himself as the second man onto the deck and the unit commander. Speaking from a hospital bed, he said he had fired his gun at an activist who came at him with a knife but was subsequently stabbed in the stomach anyway. After being thrown onto a lower deck he and another soldier jumped into the sea to escape. He did not mention his pistol being taken from him. He also said the troops expected only passive and verbal resistance.)
The soldiers, who had started to use stun grenades, then asked for permission to use their firearms. They were given the go-ahead.
However, this is not seen on the video. Indeed, it stops just as one soldier can be seen levelling his pistol at the protesters. One wonders what happened next. Why did the video stop there?
The Israelis claim that the activists got hold of two pistols and must have fired them as their magazines were found to be empty when recovered. Ben Yishai also quotes one commando as saying that the Israeli forces fired at someone holding a rifle, but no such rifle has been produced.
He says that two soldiers were wounded after "rioters apparently fired at them".
What is not clear at this stage is why so many died and in what circumstances. Did they all die on deck? In a group or one by one?
An emergency meeting of the United Nations Security Council was called
We do not see any of this on the video and one must ask whether any such video exists and if it does, then why it has not been produced. The reporter says the troops fired at "the rioters' legs". That may have been so, but it must have gone beyond that as well.
And of course, we have not yet heard any eyewitnesses from among the activists, especially the wounded. They are being held incommunicado by the Israelis.
Update: Israeli Arab member of the Knesset Hanin Zoabi, who was on the ship, has now spoken in Nazareth. She said it was clear that the Israelis "intended to cause the largest possible number of casualties... We had no plans for a confrontation." She claimed that the Israelis started firing first and demanded thatall video be released.
Ron Ben Yishai says the Israeli forces made two mistakes. They underestimated the extent of the opposition and they failed to quell it from above, by using tear-gas and stun grenades before they landed.
The general assessment in Israel at this stage therefore is that the troops went in ill-prepared and not in sufficient numbers.
They were put into a position from which they felt they had no option but to open fire and that is not a good position for commanders to place their subordinates in. Hence so much of the criticism within Israel.
It is also clear that the Israelis had little intelligence about what was being prepared on the ship.
It is reminiscent of the British assault in 1947 on the Exodus, a ship carrying Jewish refugees hoping to break the then British naval blockade on Palestine.
In that incident, too, the assault force underestimated the opposition, resorted to force, and three of the passengers died.
That event did much to undermine British rule in Palestine and to increase support for a Jewish state.