Admissions to the top universities in the US is NOT just a number’s game. The student with the highest GPA is not necessarily the one who gets accepted.
Ivy league and other top ranked schools will look at your actual grades and will look at the courses that you took.
Also your freshman year of high school will be less important than the next two or three years. Some universities will not even consider freshman year. One single C or C- in a college course taken during your freshman year might be something that they just will choose to ignore, particularly if this does not repeat.
For MIT I would be more concerned with a poor grade in a math class, but that is not what happened. I was accepted to and attended MIT with some poor grades in English and French classes, but with consistently very high grades in math classes.
Just do the best that you can from now on, and one way or another things will work out. None of us have a perfect past. None of us have a working copy of Hermione’s time turner, so none of us can go back and change that one bad grade or the one car accident or whatever we would like to have done differently.