(Source: Multiple Sources from the net)

In 1521, Ferdinand Magellan, a Portuguese explorer who was serving the Spanish crown, landed in Samar Island on his voyage to circumvent the globe. He explored the islands and named it Archipelago of San Lazaro. Magellan was killed during a rebellion led by a Datu named Lapu Lapu in Mactan Island (adjacent to Cebu Island). Spain continued to send expeditions to the island for financial gain and on the fourth expedition, Commander Ruy Lopez de Villalobos, named the islands: Philippines, after Prince Philip (later King Philip II), heir to the Spanish throne. Spain ruled the Philippines for 356 years.

In 1565 King Philip II appointed Miguel Lopez de Legazpi as the first Governor-General of the Philippines. Legazpi chose Manila to be it's capital because of it's natural harbor. Spain's legacy was the conversion of the people to Catholicism and the creation of the privileged landed class. Because of abuses and suppression of the Spaniards, a Propaganda Movement emerged with the aims for equality between Filipinos and Spaniards. The arrest of propagandist Dr. Jose Rizal and execution in 1896 gave fresh momentum to Filipino rebels to fight against Spain.

The secret society of the Katipunan, founded by Andres Bonifacio attacked the Spanish Garrison in San Juan with little success, while Katipuneros in Cavite Province headed by Emilio Aguinaldo defeated the Guardia Civil in Cavite. Aguinaldo's victories lead him to be elected as head of the Katipunan. The factions of Bonifacio & Aguinaldo fought and lead to the trial and execution of Bonifacio on Aguinaldo's orders. Aguinaldo later drafted a constitution and established the Republic of Biak-na-Bato in Bulacan province. In 1897, an impasse between the Spanish government and Aguinaldo arose. After negotiations between the two sides, Aguinaldo accepted an amnesty from the Spaniards and US$ 800,000.00 in exchange for his exile to Hong Kong with his government.

More on History 

(Source:Wiki)

A historical province known as Manila encompasses the former pre-Hispanic kingdoms of Tondo and Maynila. It became the capital of the colonial Philippines, with Manila (Intramuros) serving as the center of colonial power. In 1898, it included the City of Manila and 23 other municipalities. Mariquina also served as the capital from 1898-1899, just as when the sovereignty of the Philippines was transferred to the United States. The province was dissolved and most of it was incorporated to the newly created province of Rizal in 1901.

Since the Spanish colonial period, Manila was considered as one of the original global cities. The Manila galleon was the first known commercially traveled trade route that sail the Pacific for 250 years, bringing to Spain their cargoes of luxury goods, economic benefits, and cultural exchange.

During the American period, at the time of the Philippine Commonwealth, American architect and urban designer Daniel Burnham was commissioned to create the grand Plan of Manila to be approved by the Philippine Government. The creation of Manila in 1901 is composed of the places and parishes of Binondo, Ermita, Intramuros, Malate, Manila, Pandacan, Quiapo, Sampaloc, San Andres, San Fernando de Dilao, San Miguel, San Nicolas, Santa Ana de Sapa, Santa Cruz, Santa Mesa and Tondo. Meanwhile, the towns and parishes of Caloocan, Las Piñas, Mariquina, Pasig, Parañaque, Malabon, Navotas, San Juan del Monte, San Pedro de Macati, San Felipe Neri, Muntinlupa and the Taguig-Pateros area were incorporated into the province of Rizal. Pasig serves as its provincial capital.

In 1939, President Quezon established Quezon City with a goal to replace Manila as the capital city of the country. A masterplan for Quezon City was completed. The establishment of Quezon City meant demise of the grand Burnham Plan of Manila, with funds being diverted for the establishment of the new capital. World War II further resulted in the loss most of the developments in the Burnham Plan, but more importantly, the loss of more than 100,000 lives at the Battle of Manila in 1945. Later on, Quezon City eventually served as the national capital from 1948-1976. It was reinstated back to Manila through Presidential Decree No. 940 owing to its historical significance as the seat of government of the Philippines since the Spanish colonial period. Presidential Decree No. 940 states that Manila has always been to the Filipino people and in the eyes of the world, the premier city of the Philippines being the center of trade, commerce, education and culture.[9]

During the war, President Manuel L. Quezon created the City of Greater Manila as an emergency measure, merging the cities of Manila and Quezon City, along with the municipalities of Caloocan, Las Piñas, Mariquina, Pasig, Parañaque, Malabon, Navotas, San Juan del Monte, San Pedro de Macati, San Felipe Neri, Muntinlupa and the Taguig-Pateros area. Jorge Vargas was appointed as its mayor. Mayors in the cities and municipalities included in the City of Greater Manila served as vice mayors in their town. This was in order to ensure Vargas, who was Quezon's principal lieutenant for administrative matters, would have a position of authority recognized under international military law. The City of Greater Manila was abolished by the Japanese with the formation of the Philippine Executive Commission to govern the occupied regions of the country. The City of Greater Manila served as a model for the present-day Metro Manila and the administrative functions of the Governor of Metro Manila that was established during the Marcos administration.

On November 7, 1975, Metro Manila was formally established through Presidential Decree No. 824. The Metropolitan Manila Commission was also created to manage the region.[8] On June 2, 1978, through Presidential Decree No. 1396, the metropolitan area was declared the National Capital Region of the Philippines.[10] When Metro Manila was established, there were four cities, Manila, Quezon City, Caloocan, Pasay and the thirteen municipalities of Las Piñas, Makati, Malabon, Mandaluyong, Marikina, Muntinlupa, Navotas, Parañaque, Pasig, San Juan, Taguig, Valenzuela and Pateros. At present, all of these municipalities except for one have become an independent charted city, only Pateros remains as a municipality.