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There are three types of conflict in fiction, man vs man, man vs nature, and man vs self. Man vs man and man vs nature are not particularly interesting in themselves without the element of man vs self. Man vs man by itself is just a matter of capacity. The strong man wins. Man vs self, makes man vs man interesting. Will Rocky find the courage to come back in the fight with Apollo Creed, who clearly outclasses him as a boxer. Adrien! Love of a good woman give Rocky the boost he needs in the man vs self conflict to beat the man who should beat him. That is a story. 

If the man vs self conflict is at the heart of most stories, it is sparked by the man vs man or man vs nature conflict. Rocky does not have to find his courage at all if there is no Apollo Creed threatening to punch his lights out. The man vs man and man vs nature conflicts are catalysts for the man vs self conflict. 

The antagonist (as person) is the provider of man vs man conflict. The fundamental arc of most stories is the escalating man vs self conflict. If your protagonist had done all that they need to do in the way of providing man vs man conflict and the protagonists man vs self conflict can proceed to its final consummation without further intervention from the antagonist, then by all means put the antagonist on the end of a rocket and push the red button. 

But if the departure of the antagonist removes the impetus for the man vs self conflict, then the whole story will collapse in a puddle of goo. Only you can know which of these is true for your story.