Follow the white rabbit. Alice had to chase clues to find her way through the Wonderland, and the Matrix is no different. According to the Bible, unbelievers (whether by choice or ignorance) are separated from their Creator, blind to the truth and enslaved by their enemy. In the Matrix, sinister machines have trapped humanity in gel-filled cocoons. To maintain their existence, these cruel beings manipulate the minds of their slaves by tricking them with a false reality known as the Matrix. 1 John 4: 12-17 teaches that Satan and his demons strive to deceive man into loving the world rather than its Creator, into following destructive lies rather than the truth that makes men free. In a sense, the agents that pursue Neo symbolize this evil. The Bible also teaches that, through Christ, people can "unplug" from this life and embrace the spiritual reality that surpasses physical existence. Ultimately, at death, everything humans think is "real" will vanish, leaving them with the truth of eternity. Those who have rejected the deceptive "Matrix" and chosen instead to follow their Creator will rejoice. However, those who deny Christ to serve hell's minions have already doomed themselves to destruction.
Watch for subtle clues. It is no coincidence that the movies make use of key words to indicate spiritual principles. For example, Captain Niobe's ship is aptly named Logos, which is Greek for "Word." In keeping with this symbol of the Word of God, Logos is also understood theologically to represent the Divine Expression: Christ. In the Matrix, the Logos is designated as Mark XIV, number 14, corresponding to Mark 14: 14 in the scriptures, wherein Jesus makes preparations for the Last Supper. Captain Morpheus's ship, the "Nebuchadnezzar," is named after King Nebuchadnezzar II of Babylon as featured in the book of Daniel. The inscription on its core reads, Mark III No. 11, referencing Mark 3: 11, a Biblical passage that highlights Jesus as the Son of God. Beyond these, other symbolic names are abundant throughout the films. Consider Neo, whose name literally means "new" as in Revelation 21: 5, where Christ says, "Behold, I make all things new," declaring the restoration of His fallen creation. Lastly, don't miss the meaning behind humanity's final place of refuge: Zion.
Consider the similarities between Morpheus and God. In many ways, Morpheus is a divine "father figure" to Neo. He trains Neo, empowering him to complete his supernatural mission. He supports the prophecies of the One who is to come, the Savior of the world, and he sacrifices to ensure the prophecies are fulfilled. Morpheus nurtures Neo in times of distress and gives guidance similar to the instruction Jesus received when praying to His Heavenly Father. Furthermore, this connection is exemplified by the way Morpheus requires Neo to trust and obey him when he says, "I can guide you, but you must do exactly what I say."
Notice that Neo represents the Messiah, "The One" prophesied to save the world. Neo's "earthly" name is Thomas Anderson. Andro is Greek for "man;" therefore, Neo's last name means "Son of Man," a title Jesus used over 80 times to call attention to His divine nature as depicted in Daniel 7: 13-14. The first time viewers see Neo he is bucking the "system" by selling a computer disk to a person that says, "Hallelujah! You're my Savior, man! My own personal Jesus Christ." Furthermore, every time Agent Smith (Satan) condescendingly calls Neo "Mr. Anderson," he is actually affirming Neo's role as Messiah. Scripturally, the title "Son of Man" (Anderson) indicates Jesus' divinity (Dan. 7: 13-14), humanity (Matt. 8: 20), suffering and death (Luke 19: 10), and His future reign as King (Matt. 24: 27).
Recognize the connections between Neo's love interest, Trinity, and the Holy Spirit. Since the beginning of the Church, Christian doctrine has taught that God exists as a triune Being. Although it is nearly impossible to capture this concept in the film's symbolism, the Wachowskis made a decent attempt by including a female and highlighting her emotional bonds with two other characters. Metaphorically, Trinity's love for Morpheus as a father figure and her romance with the son figure, Neo, unites them all as one, fulfilling her namesake. Remember also that Trinity is the force that resurrects Neo after his death in the first film. This event stresses her role as a symbol of God's empowering Holy Spirit.
Note the tension between righteousness and mankind's sinful nature. One example of this is the conflict between the Architect and the Oracle, two programs that govern the Matrix. Whereas the father of the Matrix (the Architect) seeks control at the expense of freedom, the Matrix's mother (the Oracle) advocates faith and freewill. Beyond this, the Oracle is eventually exposed as the "mother" of both Neo and Agent Smith. Smith revealed in the first film that Neo represents righteousness by saying, "I believe you wish to do the right thing." Consequently, Agent Smith serves as the opposite of Neo, the Antichrist, if you will. Another way to view this tension is considering that Neo and Smith are two sides of the same being. Essentially, their combat represents the struggle people experience when choosing either holiness or rebellion. While this is a loose analogy, it does express the Biblical principle of good triumphing over evil. However, it falls short of the scriptures in several ways. The most prominent failure is the implication that Jesus and Satan are brothers, a direct contradiction of the Biblical account.
Pay attention to the fact that, like Jesus, Neo experienced death and resurrection. At the conclusion of the first movie, Neo is killed by Agent Smith in room 303. In the film, Neo is dead for approximately 72 seconds. Since Jesus was dead for 3 days (72 hours), it seems apparent that the filmmakers were drawing a clear parallel between Neo and Jesus Christ. Furthermore, Neo does not merely "come back to life." Like Christ, he returns to the world (the Matrix) transformed, possessing ultimate power over his enemies.
Realize the connection between the Ascension of Christ and Neo's flight. At the conclusion of the first movie, Neo is seen standing in a telephone booth and speaking with the artificial intelligence that created the Matrix. His message exemplifies what Christ achieved by conquering both hell and death. As though Jesus were speaking with Satan, he declares, in essence, "Your time of dominion is over." Then, stepping from the booth and putting on his sunglasses, Neo launches into the sky like Christ ascending.
Choose the red pill. Ultimately, the Matrix offers its viewers a choice, as does God. The trilogy's final movie, Revolutions, emphasizes the fact that human beings are in mental bondage, just as scripture teaches that people are slaves to their own sin. Furthermore, humans are incapable of freeing themselves. Those who know the truth about the Matrix want all humans to escape its bondage. In the films, the people of Zion have devoted themselves to rescuing as many souls/minds as are willing to accept the truth. For Christians, Jesus' sacrifice has overthrown the sinful nature and restored humanity's broken relationship with God. Like Christ, Neo willingly sacrificed himself to create peace between man and "the Source" (God). Neo becomes Agent Smith for a time, just as Christ became sin on humanity's behalf (1 Peter 2: 24). In the end, the Matrix is restored and few differences are apparent. Despite this clever deception, however, the fact remains that the Matrix (the world) will never be the same. A revolution has taken place. The enemy has lost its grip. Those still plugged into the Matrix now have a choice between liberating truth and cruel lies that rob them of reality. After Christ's resurrection, the world appeared, in most every respect, the same as it did before he died. Even so, Jesus' revolution loses none of its power when overlooked, for His sacrifice has given mankind the choice to reject their sinful nature and embrace His love. In God's presence, humans find transformation and incredible power over the mind-corrupting Matrix around them. To quote Morpheus, "Unfortunately, no one can be told what the Matrix is. You have to see it for yourself..."