After completing his education, he enrolled at the Royal Military Academy graduating from the same in 1938 as a second lieutenant. His first posting was in the town of Mankabad.
In the years to follow, he rendered his service to the Egyptian army, both as an officer and teacher. His first battlefield experience was during the 1948 Arab-Israeli War in Palestine. Though the Egyptian forces were successful in securing Fauja, they had to give up on the same after the negotiations between Israel and Egypt.
Post war, he took up the role of the instructor yet again. Meanwhile, he began to form a nationalist group of young military officers who strongly supported revolution. Syrian coup d'état was inspirational for him as he longed for a similar thing in Egypt.
He expanded his revolutionary pursuits and along with the help of three fellow officers, Zakariyya Muyi al-Din, Abd al-Hakam and Anwar el-Sadat, he formed the Association of Free Officers.
With fourteen members from various other politically active organizations, he formed Free Officers' founding committee and was elected as its chairman. The main agenda of the organization was to oust the British and Egyptian royal family from the country.
By 1952, the number of members in the Free Officer rose to 90. Same year, he planned a bloodless coup d'état, which resulted in ousting the monarchy and gaining independence of the army. King Farouk I and other monarchist leaders were allowed to go in exile instead facing a public execution.
The Republic of Egypt was declared on June 18, 1953. Major General Muhaammad Naguib served as the President while former Prime Minister Ali Maher retained his position.
A Revolutionary Command Council was formed of which he served as the Vice Chairman. His radical reforms and policies however did not go well with Maher who resigned from his post which was taken over by Naguib.
In 1953, following opposition from Naguib, he deposed the latter of the duties and put him under house arrest, while himself emerged as the Prime Minister and RCC Chairman.
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Protests broke out by members of the Muslim Brotherhood which called for reinstatement of Naguib. Having no option, he released Naguib but not before making Amer Commander of the Armed Forces.
Barely saving himself from an assassination attempt, he ordered the arrest of thousands of members of Brotherhood and those loyal to Naguib. Naguib on the other hand was put under house arrest. He then became the unquestionable leader of Egypt.
Having a small following of people, he toured the country widely to gain support. He controlled all media publications and sought to win the love of the countrymen by using flattery terms in his speeches.
In 1956, he formed a new constitution under which Egypt became a socialist Arab state with a one-party political system. Islam was declared as the official religion of the country. In the subsequent elections, he gained support of all Egyptians, for whom he was the only candidate for the post of the President.
With him as the titular and actual head, Egyptian economy seemed to get bright and prosperous. He gained monetary support from Britain and US for building Aswan Dam, which he reassured, would enhance the industrialization process.
While he continuously vouched for Arab independence from British, he started developing cordial relations with the Soviet Union, a move that irked US President Eisenhower. Both UK and US withdrew financial aid towards the building of dam.
Furious at the withdrawal of support, he announced the nationalization of Suez Canal and promised to pay British and French shareowners their share. Fearing his intention of forming an Arab alliance that would cut off oil supplies, British prime minister formed a secret society with France and Israel and planned to attack Egypt all at once.
On October 29, 1956, the Israeli Army invaded Egypt. Two days later British and French troops bombed Egyptian airfields and landed at Port Said. Meanwhile, Israelis captured the Sinai Peninsula.
The events sent a wave of fury amongst other nations, primarily US and Soviet Union who demanded cease fire and evacuation of the British, French and Israeli forces. By March 1957, all the forces retreated and the prisoners of war were relieved.
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The Suez crisis enhanced his political status and reaffirmed his position as the President of Egypt. Towards the end of the year, he nationalized several British and French industries including the tobacco, cement, pharmaceutical, and phosphate.
Furthering his economic development streak, he increased agricultural production and investment in industrialization. It was during his reign that the middle class took important political and economic positions and women were offered more freedom and rights.
In 1962, with an aim to adopt socialism, he introduced the National Charter and a new constitution, which highlighted on universal health care, affordable housing, vocational schools, greater women's rights, a family planning program, as well as widening the Suez Canal. This led to an increase in the percentage of government ownership of Egyptian business.
In 1965, he was re-elected for a second term as the President, as he was the only candidate. While his political opponents were forbidden by law, his party members were considered mere followers.
The Egyptian-Israeli war of 1967, popularly called Six Day War, led to the destruction of the Egyptian air force and the evacuation of the Egyptian army from the Suez Canal. Following this, he attempted to resign but was forced to remain in office.
He took on additional roles of prime minister and supreme commander of the armed forces. He then commenced War of Attrition to reclaim the territory captured by Israel. In 1970, under the US sponsored Roger Plan, the Israeli forces finally retreated.