"come across" as in, "He came across his friend at the mall."

He unexpectedly saw/met his friend at the mall.

for something to "come over" someone as in, "What has come over her? She is suddenly laughing and is not stopping." 

What does she think is funny? She is suddenly laughing and not stopping.

Why is she suddenly and strangely acting this way/feeling this way? She is unexpectedly laughing and not stopping.

something "to come" as in, "In the days to come, there will be more trouble."

In the following/upcoming days, (I am predicting that) there will be more trouble. 

In past days, (I am predicting that) there will be trouble. 

"come to terms with" as in, "He finally came to terms with the fact that he would get older no matter how much he did not want to."

He finally accepted that he would get older even if he didn't want to.

He finally realized the fact that he did not want to get older.

"Come again?" as in, A: "Look at the cat over there." B: "Come again?" 

A: "Look at the cat over there." B: "The cat came back again?"

A: "Look at the cat over there." B: "Can you repeat what you just said? I didn't hear you."