Note: This was my answer on Quora that was deleted by the moderators without even providing notifications and reasons for such decision.
Which countries have invaded, colonised, and committed atrocities in the Philippines over the past 200 years?
There were several countries that invaded the Philippines for the past 200 years (1818–2018) and throughout this period, a lot of inhumane atrocities have been committed against the Filipino people.
The archipelago went through a lot of invaders: Spanish, British, Americans and Japanese. The most brutal would be during the Japanese Occupation where soldiers without second thoughts raped women, killed babies using a bayonet and ruthlessly killed Filipinos.
SPANISH COLONIAL PERIOD (1521–1898)
In 1818, the Philippines was still under the colony of the Spain Empire which began due to the arrival of the Portuguese explorer sailing for Spain Ferdinand Magellan (the first European to cross the Pacific Ocean) in 1521 and ended in 1898 due to a revolution.
Taxation and Forced Labour
Spain established the encomienda system (very similar to Feudal system) that originally aimed to reduce abuse of the labour forces but later one became a form of slavery itself.
What is encomienda?
The crown provided grants to conquistadores (leaders of Spanish conquests), soldiers, officials and natives from noble birth the authority to collect tribute in a forms of treasures, lands and currency or labour force from the people they rule over in exchange that they will protect and govern them under the Spanish crown (military, judicial and local governance) and instruct them of the Christian faith.
Many Filipinos were forced to sell their lands at very low costs when asked to sell. This was in addition to paying unreasonable amount of taxes and forced strenuous labour without wages.
Initially, conquistadores treated indios (indigenous people) as slaves. This was stopped in 1670 by the Spanish crown. Later on, many people fell into debt due to the high taxation imposed on them. They were forced through violence to be enslaved to do manual labour in exchange. Due to public outcry and ecclesiastical intervention, word has been sent to the King. Since the Christian faith states that everyone is created equal and under the rule of the current King of Spain states that no slavery must be present, slavery was finally abolished in 1820.
Another case of slavery is the Trans-Pacific Slave Trade. were indios were transported and sold to Latin America. They were referred to as indos chinos. (“Chinos” is the term for the enslaved people from the Indian Ocean and the Pacific.) Indos chinos refer specifically to enslaved indigenous people from the Philippines and under the protection of the Spanish crown, they are legally cannot be traded as a slave. 
Agriculture of tobacco in the northern regions was a profitable venture. The increased revenues cultivated from the tobacco industry in the Philippines has lead to Mexico’s independence in 1781. All the profits gained was never brought back to the country but instead caused severe hardship to farmers of the lands.
The Spanish government had no intention of educating the Filipinos for self-governance. They established the schools exclusively for Peninsulares (Spanish nationals), Ilustrados (educated upperclass Filipinos with European Nationalist ideals) and some Mestizos (European blood mixed with native) in the archipelago.
Feilding Star newspaper published an article in 1898 about the underground state prison in Intramuros (Central Manila), a dungeon called Black Hole, three feet square in size. Practically burying the person alive without providing food or water and left a small hole to breathe.
Morning Post published an article in 1897 about the ruthless shootings of natives simply because the person possess such a large asset or having sympathy towards the rebellion – neither was enough reason to end ones life by shooting them multiple times.
AMERICAN OCCUPATION (1898–1946)
Right after the revolution and declaration of independence in 1898, the Philippines found itself under the American Occupation. The Treaty of Paris marked the end of Spanish empire. It relinquished all colonies of Spain and sold it to America for $20M, which included the Philippine archipelago.
The US took hold of the country and imposed its American ideals and government until they declared the long awaited independence of the Philippines in 1946.
1.4M Filipino Genocide (1899–1905)
The genocide was a buried part of history in the Philippines. It was forbidden between 1900–1946 to discuss anything against the Americans. It began when US declared war against the Philippines and the resistance lead by the first Philippine President Emilio Aguinaldo insisted the country’s independence rather than a change in colonial ruler. American soldiers obviously had a higher leverage due to combatant skills and steady supply of military equipment. Filipinos on the other hand just finished the 1898 Revolution, lost so many men and ran out limited combative supplies.
The US resorted to brutal measures as well by burning villages, implemented concentration camps with free fire zone policies (tortured and shot), tortured suspected guerrillas, slaughtered random civilians, spread epidemics such as cholera and malaria, and caused agricultural catastrophes to ensure food shortages.
In 1900, still during the war, America declared the archipelago under President William Howard Taft that started a pacification campaign to change the government which eventually won over the native elites who disagreed and did not support the rebellion. This lead to the victory of the US in the Philippine-American War. 
Death count was estimated between 1.4 to 3M Filipinos when it overlapped with the Japanese Occupation during World War II.  In such a short period, an estimate of over 5,000 battles occurred during the Phil-Am War.
JAPANESE OCCUPATION (1941–1945)
The Philippines was still under the American Occupation when World War II broke after the Japanese attacked Pearl Harbour on December 8, 1941. The Philippines at that time was an important Air Base of the US in the Pacific. General Douglas MacArthur advised Commonwealth President Manuel L. Quezon to declare Manila as an Open City on December 26, 1941 to avoid further destruction. By January 2, 1942, the Japanese entered and captured Manila.
Over 76,000–80,000 insurgents were forced to walk from Manila to the northern region of Luzon in Bataan where the concentration camp has been established. The distance was over 120km and approximately 18,000 people died due to thirst, hunger, exhaustion and severe physical abuse.  Approximately 400 captured Filipino soldiers were executed together under Colonel Masanobu Tsuji even after they have surrendered.
Comfort Women (13–15 years old)
Approximately 1,000 women were sexually enslaved by the Japanese soldiers in camp sites. They were forced to work on the fields during the day and was raped multiple times at by 5–30 men every night. They were tortured, beaten up, burned by cigarettes and cut up open.
Rape of Manila
In a short span of 28 days February 1945, 100,000 were burned, bayoneted, bombed, shelled and shrapneled dead. The Japanese soldiers have not only bombed and destroyed the city of Manila that held over 300 years of heritage from Spanish culture, it also crushed the souls of women whom they treated as inferior beings and relentlessly raped and killed; Stripped off every respect and turned it into insignificant dust particles.
With rape on the streets and everywhere else, the Bayview Hotel became Manila’s rape center. After the dirty deed was done, nipples were sliced off, and bodies bayoneted open from the neck down.
Read: The Rape of Manila
Many babies were killed through the use of bayonets during WWII by the Japanese soldiers all throughout Asia. The most famous one is the Nanking Massacre in China. The Philippines was not spared from such atrocity by the Japanese soldiers who also suffered from the war. It was believed that such war crimes occurred between 1944–1945 just before it ended.
A few accounts of first hand witnesses retelling the story of infant killings:
“Unborn babies ripped from their mothers’ wombs provided sport: thrown up in the air and caught, impaled on bayonet tips.”
“During the trial of Tomoyuki Yamashita, the general under whose command many of these war-time atrocities were committed, many mothers testified that “babies had been torn from their arms, tossed high into the air, and, when falling, were caught upon the up-thrust bayonets of Japanese soldiers standing nearby.”