It describes all the way the SQL could be executed, then choses the faster plan. For example: if you're looking for the user row with user_id xx, do you read the full table then filter it (you have to look at all the rows)? Or do you use the dedicated data structure to do so (an index will enable to do it in the logarithm of the number of rows)?

A lot more can be done: choosing the join order, choosing the join strategies, pushing the filter predicates at the source, etc. That's the vast topic of SQL optimization.