The death of his father, Phinehas, was prophesied earlier already. The Bible says that it was actually God who wanted to kill them because of their wickedness. The wicked deeds of Phinehas and Hophni were extreme. They despised the offerings of God and violated His Law, they slept with women who assembled at the door of the Tabernacle of Meeting, and they didn't listen to their father's reproof; because it says that God desired to kill them. Eli himself was guilty of knowing of their evil deeds and yet not restraining them. God's displeasure is evident in His disclosure to Samuel: "I have sworn to the house of Eli that the iniquity of Eli's house shall not be atoned for by sacrifice or offering forever." (1Sa 3:14 NKJ)
The war against the Philistines, the killing of the Israelites in thousands, their defeat; the death of the priests, and the capture of the Ark might have portended dismal days ahead in Israel's history to Phinehas' wife. She might have thought it was all over now. However, the fact was that it had only begun. The next chapter shows the single handed victory of the Ark of the Lord unaided by human hands. God struck the Philistines in their own territory and also punished their gods; they had to soon decide to send the Ark away. Then, when the Ark arrived in Israel, there were more deaths numbering in thousands because the people violated God's command about the Ark by looking at it. All through, it was a time of cleansing. The Glory hadn't left, but had begun the cleansing. The Ark was finally brought to Kirjath Jearim where it remained for 20 years. During this time, Samuel began to teach the people the ways of the Lord; there was a great revival and a time of great repentance and prayer to God. God had delivered His people from oppression, lawlessness, and aimlessness; He brought peace, order, and meaning into their life. Phinehas' wife had seen a few things and interpreted them according to what she felt; but, the world has never run out of control. The failure of man is not the failure of God.