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When we examine Marlowe's play, we have to note that Marlowe shaped this well-known story into an Elizabethan tragedy. Therefore, there is a measure of deservedness in the tragic end, but it is also based on the hero's exceptional qualities.

Marlowe's Faustus is introduced as a man highly trained in the medieval quadrivium. But he is also a man with the Elizabethan desire to know more than traditional studies affords. His first thought when he contemplates necromancy is that it could "resolve him of all ambiguities." He seeks not just knowledge, but the type of knowledge that would allay any thinking person limited by human conditions. After he trades his soul, Faustus ends up learning only those things about astronomy and exploration of other parts of the world that the humanists were already bringing into human knowledge. The ambiguity that Faustus cannot resolve involves self-knowledge and knowledge of his creator. This ends up defining his greatness (his desire to know) and his fall (his missing the mark regarding how to gain that knowledge).

A few flaws in Faustus are apparent from the first scene, most notably his selective reading of the Bible. He is too hasty in his reading and fails to see subsequent lines of comfort about sin and salvation. This arrogance remains with him. He assumes his sin is too great to be forgiven, suggesting that God could forgive Satan but not Faustus. As in his earlier studies, Faustus assumes his own greatness (even in sin) makes him out of reach even of mercy.

As he nears his end in Act 5, Faustus repeatedly contemplates and speaks of seeking forgiveness and repenting. However, he never brings himself to ask for forgiveness. He describes but does not perform acts of repentance, and therefore, he cannot be saved. He quotes from Ovid's Amores, a text that isn't quite the right one for when one faces death. As he calls out in his last moments that he wishes he'd never learned to read and that he would burn his books, he again displays a fundamental alienation from his true condition and the cause of his damnation. Faustus brings his end on himself due to lack of self-awareness, and one can lament the loss of a man of such potential, but it's hard to see him as someone other than a typical Overreacher whose hubris brought him down.

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This is an interesting question, and of course is answered differently in the many versions of this legend which have been published since the 16th century.  In some the doctor is damned, in others he is saved by various means for various reasons.  My personal opinion would be no, he does not deserve damnation.  The reason one could argue that he does is that he chooses of his own free will to make his pact in order to get what he wants, no matter the cost.  What he wants is knowledge, the same as the tale of Adam and Eve.  On the other hand, Doctor Faustus is tricked with subtle lies, also the same as Adam and Eve.  Where in the Bible death comes through the actions of the first humans, and damnation becomes possible (perhaps probable) for humans, there is a way out offered by the God of the story.  To me, this should also be an option for Faustus, for the same reason- he chose to act, but his choice was conditioned by a lie told by one who intended to harm him (Mephistopholes).

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