"In the midnight" is not a correct expression. Because midnight is a specific point in time rather than a period of time you cannot be "in" it. You would say "at midnight" rather than "in midnight" and we would not use the definite for this word.
But "at midnight" and "in the middle of the night" are not equivalent either. At midnight specifies a specific time (0000hrs, 12.00am) whereas "in the middle of the night" means at any time overnight. Typically it implies that she showed up at an inconvenient time when one would usually be sleeping.
That is using the word midnight as an abstract adjective. The word midnight means 0000hrs, though like other words can sometimes be used more loosely.
That aside, midnight and "the middle of the night" are not interchangeable in English which is the point being made above. As much as anything else "the middle of the night" used literally implies the mid point of nighttime which is not always 0000hrs, and which shifts depending on the time of year, location, daylight savings time etc.
In addition to that "in the midnight" is never correct gramatically.