Here is the timeline of events that the Israeli navy arrived at in its investigation, as reported by Ha'aretz:
Monday, 4:30 AM operation on Mavi Marmara begins. It was targeted because "of the presence of hard-core activists including members of the IHH." Operation was supervised by Navy chief Eliezer Marom and the head of naval commandos, Lt. Col. A., who were on vessels next to the Marmara.
First four commandos who rappelled onto the ship were attacked with bars, axes, and knives. Team leader had his personal weapon taken away and activists were pointing it at his head. After jumping off the rope, the fourth commando shot the activist holding the gun. This took place 20 seconds after the first commando had landed. The commanders of this first unit to land were among those to land first.
10 more soldiers were able to land, after the original rope was fixed by one of those who had already landed. 10 more soldiers rappelled onto the ship. They cared for the wounded and took over the upper deck of the ship.
4:32 AM Lt. Col. A. gives orders by radio to use live fire (in the article, this event appears after other incidents, but the narrative explains that the order was given "two minutes after the incident had begun")
4:36 AM: a second force landed from another helicopter, led by a major. Commandos on board the ship realize that 3 soldiers are missing; they begin a search for them. Naval commando chief Lt. Col. A. boards the ship along with dozen other soldiers who climbed aboard from boats or landed from a 3rd helicopter.
During the search for the missing soldiers, there is "limited shooting" on the bridge and in the lower deck, until the 3 missing soldiers are recovered.
Soldiers reported that they were fired upon (time not mentioned in summary of report). At least two commandos suffered gunshot wounds. 9mm casings were found - this is ammunition not used by the commandos, so the conclusion was that these were fired by people on the ship. The captain of the Marmara told the naval commando chief Lt. Col. A. that guns used by activists were thrown overboard before the complete takeover of the ship by the commandos. Several handguns and an M-4 rifle were taken from soldiers.
Altogether between 60-100 activists were involved in the fighting. They were apparently well-trained, judging from the weapons they had and code books which were found containing orders passed from group leaders. The rioters included Turks, Yemenis, Afghans and one Eritrean; all were experienced in hand-to-hand fighting. Even after shots were fired, some of them did not retreat.
The security forces had trained extensively for the operation, with a ship at sea holding 50 soldiers playing the role of activists. The scenario envisioned was more like a demonstration at Bil'in - a village on the seams of Israel's security fence ("wall").
Commandos were not prepared for the possibility of dozens of rioters attacking them as they landed.
The report does not explain at which points exactly the 8 other activists were killed. It claims that all of these casualties were of the hardcore, trained fighters.