I would not worry too much about the difference between "I will do this" and "I am going to do this" for now.  There is a slight difference, but it is not important at your level.  There are more important things.  

The "going to" form is used to express predictions or intentions.  So technically you cannot say "What will you do", because it is either asking what he expects that he will be doing (prediction) or what he intends to do (intention), so the 'going to' form should be used: "What are you going to do?"

See:

http://www.grammaring.com/be-going-to-for-predictions

http://www.grammaring.com/be-going-to-for-intentions

and this summary:

http://www.grammaring.com/sites/default/files/images/cheatsheets/will-be-going-to-present-continuous.jpg

http://www.grammaring.com/the-difference-between-will-be-going-to-and-the-present-continuous-for-future-events

The "going to" form has more a sense of planning than the simple future. The simple future is for a more spontaneous action.

So if he is asking him this question, he is likely asking him what he is planning to do.  So he is asking him to think about it and plan it in his head. The simple future, according to the grammar, is more for something you had not planned.

But actually I think in some cases you could actually use it, if you were asking about what would be his sponaneous reaction rather than his planned action.

The difference is fine, I would not worry about it at this point.