There are many allusions in the lines 89-98 to the weakness of God and his subjects, who Faustus somehow thinks he can harm before he falls. He speaks of combat with weak Menelaus, perhaps symbolic of God's subjects, who cannot produce magic, but only dull words. He claims he will wound Achilles - a near immortal - perhaps even representative of God or faith in God. Faustus intends to weaken others' faith in God, and thus weaken God himself. Faustus tells Helen she is brighter than Jupiter (to Helen, Jupiter would be the nearest equivalent to God, since he was the most powerful and ruled the sky) - brighter than the pure light of God. He seems adamant to insult God and the old man, and so the old man's faith is tried by demons at the end of the scene. The old man does not suffer at the devils' hands, for he calls out to his God and is protected. Conveniently, Faustus has already left and does not witness this, and so he never does see evidence of the power of God, only the fireworks of Lucifer.
The changing of the passage from past to present to future tense suggests there is a lesson to be learned from mortals attempting immortal perfection; Helen's beauty destroyed Troy, her beauty is swaying his soul back to Lucifer, and he will soon be damned because of this. Faustus is allowing for his own damnation out of fear of pain (Mephistophilis threatens to rend his flesh if he repents) and because he feels he deserves his doom. Faustus may not even believe that God can really save him, since he has never seen any intervention of God at work. He has used Mephistophilis as a faithful servant, and he has been given everything he asks, even if his magic powers do not give him control over the world. Faustus is attempting to achieve perfection of human knowledge through the devil, and he will be (literally) consumed by it.
Faustus' soul is in flux at the point when Helen enters, even as she kisses him it (his soul) is aspiring for God: "Her lips sucks forth my soul, see where is flies!" His soul is trying to fly to God, but he does not desire salvation. He is afraid of his eventual life or "death" in Hell, and wants to avoid it. Faustus wants to be immortal, fighting a symbolic battle for knowledge. Even the allusion to the sacking of Troy is portentous, however, to the contrariness of Faustus' aspirations. As Faustus champions Helen (and therefore Hell), he wears her colors, stained by the devil, and he knows that Wittenburg (which represents all the knowledge Faustus has gained there) will fall.
As Faustus and Helen leave, we see the old man tormented by devils sent by Faustus himself. This is the doctor's repayment to the old man for persuading him to repent to God. Such cruelties to an innocent man and Faustus' enrapturement in his own illusions seem to be the ultimate dooming element of this character, and Faustus believes himself past repentence from this point.
As Faustus succumbs to Helen's kisses, he reacts as if he now has no soul to save; he pledges himself to the devil once more, to the pursuit of destruction of faith in God. This scene is Faustus' own attempt to distract his mind and heart from the real longing for salvation of his soul. Within these 19 lines, Faustus reflects upon the destructiveness of Helen's beauty and its effects on the past (80-1), present (82-4), and future (85-99). The scene with Helen illustrates Faustus' strengthening of his own resolve to honor his contract with Lucifer and be damned. Faustus becomes very self-righteous, believing he alone with his faith in Helen (and hence, the devil, since his Helen here is a demonic illusion) can destroy Wittenburg, the German center of knowledge and learning. The destruction of Wittenburg relates to the destruction of Faustus himself, since Wittenburg is where his knowledge was gained, where he became corrupt and signed his soul to Lucifer. The figurative fall of Wittenburg may even hint at Faustus' suicidal tendencies, but he will not commit suicide since he fears damnation and would rather avoid it. He believes that he can somehow wound the invulnerable - which could refer to invulnerable God himself, now likened to Achilles. (87-92) When he has accomplished these terrible deeds, Faustus indirectly declares he shall be damned, for now he is beyond salvation. Faustus becomes similar to Helen in his desire for perfection; when it is achieved by mortals, it can only bring about destruction.