Rabin's tenure as Chief of Staff was marked by the rapid military buildup of the Arab nations, who were equipping themselves with Soviet arms. Rabin was occupied primarily with preparing the IDF for the possibility of all-out war. He worked to equip the IDF with American arms and with modern technologies, and prepared it for a coordinated air, land and sea strike. At the same time, he also drew up operational plans that the IDF could use at any time. All of these were put to the test in the Six Day War and played a decisive role in Israel's swift victory.
One of the focal points of tension was in the North, where Syria and Lebanon were attempting to divert Israeli water sources originating in their territory. Rabin objected to any initiative that included the conquest of territory in Syria and focused the IDF's response on hitting the mechanical equipment used to divert the water sources.
Another front facing Rabin was that against Fatah, the military arm of the Palestine Liberation Organization. Rabin took the fact that Fatah had set up bases in Syria and used them to launch attacks in Israel as his justification to act against the Syrians. Comments made by Rabin against the Syrian regime in a newspaper interview met with a harsh response, and were later seen as a factor that hastened Syria's preparations for war against Israel. In response to attacks on Israeli civilians, Rabin supported attacks on enemy civilian infrastructure targets. However, in November 1966 he authorized a raid on Samwa in Jordan that led to the deaths of many Jordanians, both civilian and military.
At the end of 1966, after Rabin had served three years as Chief of Staff, the Prime Minister decided to extend his tenure by another year.
The Six Day War
In 1967, in Rabin's fourth year as Chief of Staff, the Six Day War broke out. At the beginning of that year no one was thinking about war, and certainly not war with Egypt. The focus of tension was the continued clashes along the Northern border. In response to Syrian attacks, the Israeli Air Force was sent into action, and on April 7 shot down six Syrian Migs in an aerial dogfight. In response, Egypt, which had a defense pact with Syria, began to call up reserves. Egypt sent a military force into Sinai in violation of the disengagement agreements with Israel. Rabin saw this as an act of war and recommended that Israel call up its reserves. Egypt's President, Gamal Abdel Nasser, instructed the United Nations force to leave Sinai and then closed the Straits of Tiran to Israeli shipping. As far as Israel was concerned it was a declaration of war. The situation continued to deteriorate rapidly and war became inevitable.
Rabin had an unshakable belief in the IDF's ability to win the war, and the army under his command was ready and waiting for battle. The General Staff pushed for a preemptive strike. But Rabin understood that the government need to be given time for diplomacy. Senior figures with whom he consulted undermined his belief in the IDF's ability to launch a war without the backing of a friendly power. Torn between his recognition of the need to land a preemptive blow, and his recognition of the duty to defer to the political echelons - working around the clock and smoking incessantly - he became exhausted and simply couldn't go on. But after 24 hours rest he returned to do his job.
Public anxiety among the public during what was labeled the Countdown Period led to the foundation of a National Unity Government. Prime Minister Levi Eshkol was forced to give up the defense portfolio to Moshe Dayan who was appointed Defense Minister. On June 4, the government decided to go to war and on June 5, in an operation involving almost all its planes, the Air Force attacked the airbases and air forces of Egypt, Syria, Iraq and Jordan, dealing them a mortal blow. This crushing attack opened the way for armored corp and infantry to move into the Sinai Peninsula. The Egyptian army was overcome within days and withdsrew to the Suez Canal. In the wake of Jordanian attacks around Jerusalem a second front was launched. Two days later, IDF forces had taken over the entire West Bank and East Jerusalem, and had reached the Western Wall. On the fifth day of the war, once the Egyptian and Jordanian armies had been defeated, the IDF attacked the Syrians in the Golan Heights. Once the Golan Heights had been taken a cease-fire came into effect and the threat to the northern settlements was removed.
Rabin monitored the Air Force operation from Air Force headquarters. Once the results became clear he moved to the "Bor" - the IDF's underground command center. From there he supervised the execution of the battle plans, and from there he headed out for tours of the battle arenas. With the exception of a visit to Jerusalem after the liberation of the Western Wall, Rabin refrained from high-profile visits and gave few interviews. At the end of the war it was a different Israel - the territory controlled by Israel had grown three fold and it now had responsibility for 1.5 million Palestinians. The dispute over Israel's borders, which had ostensibly ended after the War of Independence, had now been reopened.
For his part in the victory, the Hebrew University of Jerusalem decided to bestow upon Major General Yitzhak Rabin an honorary doctorate as an expression of the gratitude the Israeli public felt toward the architect of victory.
In a speech summing up the campaign, Rabin, without arrogance or glee in the victory, stressed the heavy cost of the war to both the victors and the defeated nations.