The second soldier was surrounded by twenty passengers in two groups. One group attacked him when he landed on the ship’s roof. He fired one shot at an activist holding a knife before becoming subdued. The passengers seized his gun and beat him as he attempted to fight them off with his back to the hull. He was picked up by his arms and legs, and thrown over the hull. He tried to hang on to the hull with both hands, but was forced to let go when the passengers beat his hands and pulled him down by his legs. He was then surrounded by another group, stabbed in the stomach and dragged into a lounge while being beaten.
A third soldier who was lowered onto the deck saw a passenger waiting to attack him with an iron crowbar. After shoving him away, he was attacked by four more passengers, one of whom wrapped a chain around his neck and choked him until he lost consciousness. He was then thrown onto the bridge deck, where he was attacked by about twenty passengers, who beat him, cut away his equipment, and dragged him into the lounge.
All three soldiers were severely wounded and bleeding heavily. Two of them had their hands tied, and a third was unconscious and went into convulsions. During their captivity, they were subjected to physical and verbal abuse, photographed and filmed. One of the soldiers said that he was beaten after he began moving and yelling that one of the soldiers needed a doctor, and another said that he was placed on a couch, beaten, and threatened that he would be beaten every time he moved. Eventually, some of the apparently more moderate passengers intervened and protected the soldiers. Two soldiers were given water and one, who suffered from a critical stomach gash was given a gauze pad. A Turkish doctor cleaned the blood off their faces and tended to facial cuts.
Israel commandos reported that at least two of the captive soldiers had their sidearm taken, and that there was live fire against them at a later stage. According to the IDF, the passengers also used firearms that they had brought along with them—investigators later found bullet casings that did not match IDF-issued ammunition. According to the IDF, the second soldier coming down the rope was shot in the stomach, and another soldier was shot in the knee. The passengers also seized three stun grenades from the soldiers.
After the third soldier was thrown from the roof, the commandos in the chopper received permission to open fire. They fired pistols, and the passengers dispersed to the front and back of the roof after taking casualties. An IDF medical officer on board located a secure spot, and oversaw treatment of injured soldiers.
A second helicopter carrying 12 soldiers arrived over the ship, and as passengers attacked the commandos, they were repulsed with gunshots aimed at their legs. The soldiers from the second helicopter finally managed to slide down and took over the front of the roof, then secured the lower decks. Passengers attacked them, and were dispersed with shots to the legs. Fire was exchanged from both sides, then a third helicopter arrived, with 14 soldiers, and both forces began moving to take over the ship. They were attacked twice by passengers, and responded with gunfire. Thirty minutes later, the commandos reached the bridge and took control. The captain instructed all passengers to enter their cabins. The speedboats trailing the ship approached again, and the passengers who remained free hurled objects at them. The soldiers inside the boats opened fire, taking careful aim to hit the resisting passengers and forcing them to disperse. The soldiers boarded using ladders, were met with resistance, and responded with live fire. They fought their way to the roof, where they met up with the rest of the force.