The movie is a modern day punk parable of the Gospel of Jesus Christ. Neo (One) Thomas (doubting) Anderson (son of man, andros)  is the Christ figure. Finds himself by studying the scriptures represented by the computer. Php.2:8; Morpheus is John the Baptist and baptizes Neo who awakens to the Truth and is unplugged and flushed away by the world.

Their ship, the Nebuchadnezzar (the church) takes him in and through acupuncture, Dozer, gets his spiritual muscles working once again. Dozer and Tank are James and John the sons of thunder. Mouse is Peter.
Trinity the Holy Spirit. Zepher is Judas. Mr.Smith is the devil.
The Oracle is the OT, she is baking cookies and smoking, the OT shows the good and bad sides of people. To prove who Christ is you go to the OT. Notice as well the children in the waiting room representing eastern religions, very childish in nature and Neo is full grown about 30 yrs old. Lk.3:23; Tank loads Neo with programs that give him instant ability to perform things like Kung Fu etc. Then he had to practice those abilities in the 'construct', with Morpheus as his sparring partner. Similarly with the patterns found in the Bible, you have the ability to memorize whole books. Then you need to get in the construct and practice teachingwhat you've memorized with other Christians so your both prepared for the opportunity to teach the lost when it arises. If your not prepared by practicing with other Christians, you won't be looking for a study with the lost. Iron sharpens iron. Zephyr betrays everyone, Morpheus gets caught, Neo goes in for the rescue, knowing he was going togive his life to safe Morpheus. Jn.15:13; This is how he learns who he is, by putting his faith to the test. Neo realizes you cannot fight fire with fire and win, he couldn't defeat Mr.Smith in the subway, so he runs, only to be gunned down in room 303, 'crucifixion'
Trinity whispers get up, "the resurrection". Now to defeat Mr. Smith, Neo stops the bullets in flight, Mt.28:19  Then runs and dives into Mr. Smiths body turning on the light and destroying evil with love. Rom.12:17-21; Movie ends with Neo stepping out of the phone booth and pulling a superman soaring up up and away beyond the clouds.
The ascension. Ac.1:9;
There are so many other cool references throughout the movie, that makes it fun watching and spotting all the Christian applications and references. Could be good for a youth night activity. Identifying the spiritual applications for  us today. The other two movies bombed big, they are not spiritual in any way but  very immoral. Not recommended.
But the Matrix is a cult classic because your soul picks up on the gospel being  presented which resonates deep within the heart. But the violence hides the  under lying story so it takes a Christian to explain it to the lost, which creates  a great dialogue over a modern movie concerning Christ Jesus.
 The movie came out easter weekend in 1999 but three weeks latter the Columbine shootings took place and all the churches blammed the movie for the killings, so they banned all their kids from watching it. The kids still saw it but because they couldn't talk about it at church, the spiritual lesson was lost and so was a great evangelistic opportunity. But that opportunity is still with us because the movie is a classic.