Though the destruction of Egyptian early warning radar and ELINT sites was an ongoing goal during this period, known as the War of Attrition, the raid was as much prompted by a wish to send a "message" to Egypt as it was the actual destruction of the military targets. IDF Chief of Staff Chaim Bar Lev and Minister of Defense Moshe Dayan together decided that Egypt should be shown that no Egyptian position was safe, no matter how well-fortified or impregnable. As a target, Green Island fulfilled both goals. Green Island could have been more easily attacked by Israeli artillery or aircraft with less risk to Israeli life, but a commando raid would send a clear message and, it was hoped, have a negative effect on Egyptian military forces' morale.
The plan called for the Naval Commandos, using Zodiac inflatable boats, to lead the first of two waves in the assault. The second wave, by Sayeret Matkal, would consist of commandos, command and control and medical teams, and an extraction team. The second wave commandos would arrive to carry the fight just as the first wave ran low on ammunition.
The first wave surfaced at the island 8 minutes behind schedule, at 0138. The delay was caused by a more difficult swim than anticipated due to the currents. The first team breached the barbed wire allowing the second team to move in and counter the initial Egyptian response. The third team then crossed a small bridge and destroyed a defensive and observation tower and radar facility. The fourth team cleared a building to the north. Half the raiders cleared or blocked the southern half of the island, the fortress, while the other half eliminated the radar and anti-aircraft equipment. This was complicated by the fact that most of their hand grenades were rendered useless by the swim at deeper than expected depths due to each man's heavy load. This breaching of the island's defences was supported by a separate Naval Commando team providing covering fire and diversion with a bazooka and a light machine gun from a small rock outcropping just south of the island, having reached it by Swimmer Delivery Vehicles (SDV). At this point the commander of the first wave, Lieutenant Dov Bar, signaled the second wave to come in using a flare. To avoid catching the approaching second wave in a cross fire a second flare by Bar signaled the covering fire and diversion team on the rock outcropping to stand down and withdraw, which they did successfully. The second wave, which had been idling in their Zodiacs in the Gulf, now trailing the first wave's recovered boats, roared up to the island. They quickly set up a command post and aid station and took out the 85 mm gun emplacements.
Not much larger than a football field, all combat on the island was conducted at close range. The Egyptian response to the first wave was uncoordinated at first, then became fierce, employing heavy and light machine guns and rocket propelled grenades. After the arrival of the second wave, the efforts of the defenders became sporadic and again uncoordinated, with some jumping from bunkers into the sea, and eventually calling in artillery on their own position.
The extraction was ordered at 0225. By 0255 the teams were aboard the Zodiacs and heading for the eastern bank of the Gulf, having lost one Zodiac at the island to Egyptian artillery fire. At 0310, with the Israeli commandos still crossing the Gulf, satchel charges left on the island detonated destroying the remaining facilities. Egyptian artillery now shelled both the Zodiacs and the beachheads set up to receive them, driving several boats away and delaying their landings while they searched for alternate beaches to divert to. Another Zodiac was lost when it was abandoned by its team less than 400 meters from Green Island, but the team was recovered by helicopter at 0500 after spending several hours swimming toward the eastern shore.