Short answers, pulled from the story.
The Japanese military committed massacres against civilians in Manila between February and March 1945. At least 6,000 non-combatants died in San Agustin Church while about 2,000 more perished at La Concordia College on the 8th of February 1945.
General Tomoyuki Yamashita ordered a complete withdrawal of Japanese troops from Manila in January 1945 to preserve forces for future operations. Rear Admiral Sanji Iwabuchi ignored this order and chose to remain in the city with approximately 10,000 marines instead of retreating.
The combined death toll of civilians for the Battle of Manila was about 100,000 according to historical records. Some historians suggest that 100,000 to 500,000 people died as a result of the Manila massacre alone excluding other causes like American artillery fire.
The Bayview Hotel served as a designated rape center where Japanese soldiers rounded up women and girls from the Ermita district. At least 20 Japanese soldiers raped a young girl before slicing her breasts off and setting her and two others on fire with gasoline.
General Tomoyuki Yamashita was convicted because he made no attempt to discover or stop atrocities committed by his subordinates. He was hanged on the 23rd of February 1946 despite ordering an evacuation while Rear Admiral Sanji Iwabuchi's forces carried out the massacres.