Short answers, pulled from the story.
At least 100,000 civilians were killed during the Battle of Manila from all causes, including the massacre by Japanese troops. Some historians estimate the Manila massacre alone, exclusive of other causes, killed between 100,000 and 500,000 people.
The atrocities were primarily committed by roughly 10,000 Japanese marines under Rear Admiral Sanji Iwabuchi, who defied General Tomoyuki Yamashita's order to withdraw from Manila. General Yamashita and his chief of staff Akira Muto were later convicted of war crimes for their broader command responsibility over Japanese forces in the Philippines.
The Yamashita standard is the principle in international law that a military commander bears responsibility for war crimes committed by forces under his authority, even without a direct order, if he made no attempt to discover or stop the atrocities. It arose from the war crimes trial of General Tomoyuki Yamashita, which began in October 1945 following the Battle of Manila.
General Tomoyuki Yamashita was tried for war crimes beginning in October 1945 and convicted. He was hanged on the 23rd of February 1946 in a camp south of Manila. His chief of staff Akira Muto was hanged on the 23rd of December 1948.
Before the battle, Yamashita ordered a complete withdrawal of Japanese troops from Manila in January 1945, judging the city indefensible. However, Rear Admiral Sanji Iwabuchi and approximately 10,000 Japanese marines under his command ignored the order and chose to remain, holding the city through the Battle of Manila.
The Bay View Hotel in the Ermita district was used as a designated rape center by Japanese forces. According to testimony at the Yamashita war crimes trial, 400 women and girls were rounded up from Ermita, and 25 were selected and taken to the hotel, where Japanese enlisted men and officers raped them. Many of the victims were 12 to 14 years old.