Samson Agonistes combines Greek Tragedy with Hebrew Scripture, which alters both forms. Milton believed that Bible was better in classical forms than those written by the Greeks and Romans. In his introduction, Milton discusses Aristotle's definition of tragedy and sets out his own paraphrase of it to connect it to Samson Agonistes:
Tragedy, as it was anciently composed, hath been ever held the gravest, moralest, and most profitable of all other poems: therefore said by Aristotle to be of power by raising pity and fear, or terror, to purge the mind of those and such-like passions, that is to temper and reduce them to just measure with a kind of delight, stirred up by reading or seeing those passions well imitated. Nor is nature wanting in her own effects to make good his assertion: for so in physic things of melancholic hue and quality are used against melancholy, sour against sour, salt to remove salt humors.
Milton continues, "Of the style and uniformity, and that commonly called the plot, whether intricate or explicit... they only will best judge who are not unacquainted with Aeschylus, Sophocles, and Euripides, the three tragic poets unequaled yet by any, and the best rule to all who endeavor to write tragedy".
The reliance on Hebrew Scripture allows Milton to emphasise a plot that he feels is worthy of discussion, while the elements of Greek Tragedy allows Milton to deal with complex issues through use of choruses and messengers instead of directly depicting them in addition to softening the Hebrew characters. This merging of two forms alters Samson from a rough barbarian into a pious warrior of God.
Acts of violence are an important theme within Samson Agonistes as the play attempts to deal with revenge and the destruction of God's enemies. Michael Lieb posits that "the drama is a work of violence to its very core. It extols violence. Indeed, it exults in violence". John Coffey simply describes the action in the play as "a spectacular act of holy violence and revenge". Likewise, David Loewenstein remarks that "the destruction and vengeance depicted in Samson Agonistes, then, dramatizes a kind of awesome religious terror". Gordon Teskey describes the plot of the work when he says, "delirious violence of the hero of Samson Agonistes, who cancels the Philistine hallucination of a unified and harmonious world".
The play itself suggests the horror within the actions through descriptive phrases, including "evil news" (line 538), "this so horrid spectacle" (line 1542), "the place of horror" (line 1550) and "the sad event" (line 1551). Although Samson is the hero and he causes the violence, Elizabeth Sauer points out that "Milton devotes nearly twice as many lines to the Chorus’ reactions in the denouement than to the Messenger’s description of the catastrophe in order to deemphasize spectacle and performance and instead to highlight the interior drama while encouraging active interpretation of the reported events"
The play, focusing around the betrayal of Samson at the hands of Dalila, his wife, produces a negative portrayal of love and love's effects. Women, and men's desire for women, are connected to idolatry against God, and the idea that there is no possibility for the sacred within the bonds of marital love. Samson, who is both holy and desirous of Delila, is seduced into betraying the source of his strength, and thus betrays God. He is emasculated, through blindness, because of his sexual desires. The Chorus, after Delila attempts to seduce Samson again, criticises women for being deceptive.
Samson's argument against Dalila is to discuss the proper role of a wife but also the superiority of men. The depiction of Dalila, and women, is similar to that in Milton's divorce tracts and, as John Guillory states and then asks, "We scarcely need to observe that Samson Agonistes assumes the subjection of women, a practice to which Milton gives his unequivocal endorsement; but is there any sense in which that practice of subjection is modified by the contemporaneous form of the sexual divisions of labor?". A wife is supposed to help a husband, and the husband, regardless of the status of the woman, is supposed to have the superior status. In blaming Dalila, he rationalises his actions and removes blame from himself, which is similar to what Adam attempts in Paradise Lost after the fall. However, Samson develops through the play and Dalila reveals that she is concerned only with her status among her people. This places Dalila in a different role from Milton's Eve. Instead, she is an emasculating force and represents Samson's past failings.
Samson undergoes despair when he loses God's favour in the form of his strength. In his searching for a way to return to being true to God and to serve his will, Samson is compared to the non-conformists after the English Restoration who are attacked and abused simply because they, according to their own view, serve God in the correct way.
As blindness overtook Milton, it becomes a major trope in Samson Agonistes, and is seen also in Paradise Lost (3.22–55) and his 19th Sonnet. Many scholars have written about the impact of Milton's increasing blindness on his works. This recurrence of blindness came after Milton temporarily gave up his poetry to work for Oliver Cromwell and the Commonwealth government. He continued this service even though his eyesight was failing and he knew that he was hastening his own blindness. The correlation is significant to the Agonistes plot: Milton describes Samson as being "Eyeless in Gaza", a phrase that has become the most quoted line of Agonistes. Novelist Aldous Huxley used it as the title for his 1936 novel Eyeless in Gaza.
Samson's blindness, however, is in no way a direct analogy to Milton's. Rather, Samson's blindness plays various symbolic roles. One is the correlation between Samson's inner blindness as well as outer, the fact that he believes his "intimate impulses" to be divine messages, yet is never in any way divinely affirmed in this, unlike the rest of Milton's divinely influenced characters. Samson's inability to see that his inner vision does not correlate to divine vision is manifest in his physical blindness. It also plays on his blindness to reason, leading him to act overhastily, plus the fact that he is so easily deceived by Delila, "blinded" by her feminine wiles. It is interesting to note that some of the chorus's lines in Samson Agonistes are rhymed, thus suggesting a return of the "chain of rhymes", which itself reflects upon Samson's imprisonment.