Newcomb's Box is Empty
If we accept the premises of the Newcomb Problem, then it's not possible to receive $1,001,000 from playing this game. But you have the choice to take both boxes, and therefore the mystery-box is empty.
Once you approach the boxes to make your decision, the boxes have been determined. From this point, we know that:
(A)You cannot end this game with $1,001,000.
We know this because it's a stipulation of the problem: nobody walks out of here with both boxes full of cash. We can't violate this rule, or we are negating the premise of the paradox.
Another stipulation is the choice:
(B)You may choose to take both boxes.
If the mystery-box contains $1,000,000 and you have the option to take both boxes, then you can walk out of here with $1,001,000. But since you cannot leave with this money, and you may take both boxes, we can conclude that the mystery box is empty.
Suppose the opposite:
(C)The mystery box contains $1,000,000.
More formally:
C ∧ B -> ¬ A
A -> ¬ (C ∧ B)
¬C ∨ ¬B
So if we accept B (another stipulation of the puzzle itself) then we must accept that C is false.