The first major theme evident in the play is deception. Rather than allowing Philoctetes to decide for himself, Neoptolemus and Odysseus concoct a plan to manipulate him into coming back with them to Greece. This shows that they are willing to do whatever is necessary to ensure that the Greeks have an advantage in the war.

This leads to the second major theme of the play, which is the concept of "the greater good." It is clear that the wounded archer is suffering from physical pain and can barely move without the help of a bow to use as a crutch. However, the selfishness of Neoptolemus and Odysseus tries to overpower respect for a fellow man and common decency. This is a reflection of what psychologists call groupthink, or conformity that is especially bound by a common goal or belief.

In this regard, the other theme of the play is conformity within the military and how the military has its own rationale that is separate from universal concepts of morality. This is evident in the fact that they emphasize the importance of sacrificing one's body in order to contribute to the military's victory against the enemy. This is exemplified by the fact that Odysseus is not bothered by Philoctetes's expressions of suffering and pain.

The other prominent theme in the story is the reward one receives when sacrifices are made. Philoctetes's chronic pain is cured when he finally decides to return to Greece on his own free will and slays many Trojan soldiers. Despite the positive outcome for Philoctetes, his once-injured foot that would not heal was an analogy for the effects of war on the collective psyche of a nation; that metaphorical wounds suffered from war will never heal, even centuries later, because it will always be a constant reminder of human brutality in our shared history.