stylistic:tone, structural:reformatting
Later political career

In May 1967, Egypt began massing forces in the Sinai Peninsula after expelling UN peacekeepers and closed the Straits of Tiran to Israeli shipping. This, together with the actions of other Arab states, caused Israel to begin preparing for war. The situation lasted until the outbreak of the Six-Day War on 5 June. In Jerusalem, there were calls for a national unity government or an emergency government. During this period, Ben-Gurion met with his old rival Menachem Begin in Sde Boker. Begin asked Ben-Gurion to join Eshkol's national unity government. Although Eshkol's Mapai party initially opposed the widening of its government, it eventually changed its mind. On 23 May, IDF Chief of Staff Yitzhak Rabin met with Ben-Gurion to ask for reassurance. Ben-Gurion, however, accused Rabin of putting Israel in mortal danger by mobilising the reserves and openly preparing for war with an Arab coalition. Ben-Gurion told Rabin that at the very least, he should have obtained the support of a foreign power, as he had done during the Suez Crisis. Rabin was shaken by the meeting and took to bed for 36 hours.

After the Israeli government decided to go to war, planning a preemptive strike to destroy the Egyptian Air Force followed by a ground offensive, Defense Minister Moshe Dayan told Ben-Gurion of the impending attack on the night of 4–5 June. Ben-Gurion subsequently wrote in his diary that he was troubled by Israel's impending offensive. On 5 June, the Six-Day War began with Operation Focus, an Israeli air attack that decimated the Egyptian air force. Israel then captured the Sinai Peninsula and Gaza Strip from Egypt, the West Bank, including East Jerusalem from Jordan, and the Golan Heights from Syria in a series of campaigns. Following the war, Ben-Gurion was in favour of returning all the captured territories apart from East Jerusalem, the Golan Heights and Mount Hebron as part of a peace agreement.

On 11 June, Ben-Gurion met with a small group of supporters in his home. During the meeting, Defense Minister Moshe Dayan proposed autonomy for the West Bank, the transfer of Gazan refugees to Jordan, and a united Jerusalem serving as Israel's capital. Ben-Gurion agreed with him but foresaw problems in transferring Palestinian refugees from Gaza to Jordan, and recommended that Israel insist on direct talks with Egypt, favouring withdrawal from the Sinai Peninsula in exchange for peace and free navigation through the Straits of Tiran. The following day, he met with Jerusalem mayor Teddy Kollek in his Knesset office. Despite occupying a lower executive position, Ben-Gurion treated Kollek like a subordinate.

Following the Six-Day War, Ben-Gurion criticised what he saw as the government's apathy towards the construction and development of the city. To ensure that a united Jerusalem remained in Israeli hands, he advocated a massive Jewish settlement program for the Old City and the hills surrounding the city, as well as the establishment of large industries in the Jerusalem area to attract Jewish migrants. He argued that no Arabs would have to be evicted in the process. Ben-Gurion also urged extensive Jewish settlement in Hebron.

In 1968, when Rafi merged with Mapai to form the Alignment, Ben-Gurion refused to reconcile with his old party. He favoured electoral reforms in which a constituency-based system would replace what he saw as a chaotic proportional representation method. He formed another new party, the National List, which won four seats in the 1969 election.