Masada carries a national story, and the story and the archaeology are not the same object.
The single source. Everything narrative we have about the siege comes from one writer, Flavius Josephus, in The Jewish War. He reports that after Jerusalem fell in 70 CE a group of rebels held the desert rock, and that when the Tenth Legion finally breached the wall in 73 or 74 the defenders, he says nine hundred and sixty, killed their families and then themselves rather than surrender, drawing lots for who would do the last killing, so that the Romans entered upon the silent dead. Josephus was a former rebel commander who had gone over to Rome, writing for a Roman audience; he is a single, interested witness.
The excavation and the myth. Yigael Yadin's digs of the 1960s made Masada central to Israeli identity. Soldiers were sworn in on the summit; "Masada shall not fall again" became a slogan. The sociologist Nachman Ben-Yehuda later traced, in detail, how that national narrative was assembled and simplified from Josephus, and how the archaeology does not cleanly confirm a coordinated mass suicide. Only a small number of skeletons were found, in circumstances that do not settle the question.
What is solid. The Herodian palaces, the storerooms and cisterns, the Roman camps and the great assault ramp are all really there, and they are extraordinary. What the atlas flags is the gap between that firm physical record and the polished heroic story told over it, the story being the part that was made.