Though Neo puts his own life at risk to save the people who are important in his life, he engages in actions which would seem objectively evil in order to achieve his goals. In storming the building where Morpheus is held captive, Neo indiscriminately guns down many of the building's security officers. As stated earlier in the movie, when someone is killed inside the Matrix, they die in the real world. Therefore, Neo is killing the actual people themselves when he kills them in the Matrix. Since it is immoral to take another human life when it is not in self-defense, this complicates Neo's moral situation.

In the book Doing Evil to Achieve Good, Richard McCormick, S.J., says that there are four conditions when the evil enacted by a person in the process of doing good is justifiable. The action must either be good or indifferent in itself (not morally evil), the intention of the agent must be upright (the evil is not sincerely intended), "the evil effect must be equally immediate casually with the good effect," or "there must be a proportionately grave reason for allowing the evil to occur."

In Neo's situation, the casualties he inflicts could arguably be justified given the ends he is trying to achieve. In Doing Evil to Achieve Good, Van der Poel is said "to suggest that proportionate reason is found in a balancing of the identifiable values immediately at stake. For instance, one may not abort a pregnancy simply to avoid shame." In Neo's case, he was acting to rescue Morpheus from interrogation at the hands of the Matrix's agents, which could lead to the destruction of the last remaining human stronghold in the world.

Doing Evil to Achieve Good also relays the writings of Peter Knauer, S.J., which say that "moral evil consists in the permission or causing of a physical evil without commensurate reason." The book further explains that "the defense of one's life against an assailant is not exactly an effect, but rather an aspect of the act," and that an action "becomes a moral act through the intention of the donor." In this instance, Neo's intention was the save humanity by way of rescuing Morpheus from his captors, which in turn involved killing the building's security personnel.

This reasoning may seem irrational. However, it is important to keep in mind the difference between direct and indirect. While these terms are often associated with physical causality, Knauer claims that "the permission or causing of a physical evil is direct or indirect as there is or is not present a commensurate reason," and that when a reason is present it "occupies the same area as what is directly willed and alone determines the finis operis, so that the act is morally good."

Whether or not the reasons for Neo's actions are proportional to the ends that he is achieving is the cause for much of the ambiguity in his actions. Unfortunately, some plot information that would lend itself to clearing up the ambiguity is not available. For instance, the humans in the real world are fighting a war to end the enslavement of their race to the machines. Given that they are part of a larger war effort against slavery, Neo's actions seem to be proportional to his situation. However, Morpheus states in the movie that no one knows who originally started the war with the machines. Not knowing for sure if the humans or the machines were the original aggressors of the war prevents a definite black and white judgement of Neo's actions from being made.

Neo's experiences in this first chapter of the Matrix trilogy also create an interesting mirror image of Neo's life. When confronted by Agent Smith, Neo is asked to help bring a known terrorist (Morpheus) to justice. Given that Morpheus's actions during the war inside the Matrix really are more terrorist-like than soldier-like and that innocent people most likely suffer as a result, there is some truth to Agent Smith's characterization of Morpheus. At the same time, the agents are helping to keep humanity enslaved in ignorance, and Morpheus's actions are meant to end this enslavement. This split path involves two options which will both result in the reduction of injustice against innocents and will both result in the assistance of a cause which threatens the well-being of innocent people. When faced with this decision, Neo chooses what seems to be the lesser of two evils and the greater of two goods by helping Morpheus.