The "alternate vision" view of the barge carrying Neo at the end has been described as angelic. It also looks like the petals of a flower, notably the Lotus flower - a Buddhist symbol for two notable things here. First, the lotus blossoms unstained by the muck from which it grows (think: coppertop farm). Second, it symbolises a sharing of spontaneous generation and giving to others - akin to self-sacrifice.

Back in "Reloaded", when Neo, Trinity and Morpheus arrive with the Merovingian, you can see one of his bodyguards escorting out Sati's father - the man Neo met at Mobil ave. - probably after having finished the transaction to smuggle Sati into the matrix, which her father mentions to Neo in this film.

Neo's journey to the machine city and subsequent battle with Smith has many parallels with the new testament. Firstly, when he and Trinity fly over the clouds it mirrors the ascension of Christ into heaven. Secondly, Neo walking along the gangway where he is confronted by the Deus Ex Machina is similar to St. Paul on the road to Damascus where he was confronted by God, and lastly Neo's fight with Smith is effectively Armageddon battle of God against the devil, and leads to the end of one world and beginning of the next.

The train that trainman leaps in front of has "Loop" on it. This is another Chicago reference (e.g. all of the street corners in the first film are actual intersections in Chicago). The Chicago "L" or "elevated" train (elevated is shortened to L) has a large circular section that runs around the City center. This is called the "Loop." Relevant here of course as Mobile Ave. is also a loop, trapping Neo.

Several things in the movie relate to the video game 'Enter the Matrix.' Two examples are when Niobe says she saw the Oracle right before the EMP was fired from the Hammer. One of the video game's cut scenes are when Niobe and the Oracle have a meeting. Niobe also mentioned when she was cornered by sentinels. You get to play that level in the game where you are being chased by the sqiddies. Also in Reloaded when the power plant is destroyed, that is also one of your objectives in the game as Niobe. The Trainman and Niobe also have a brief encounter in the game. There are many other examples, but you need to play the game to find them out.

The idea of Neo becoming blinded and then being able to "See" life force is identical to a major plot event in "Dune Messiah", Book 2 of Frank Herbert's Dune. The major character with god-like powers is struck down and blinded through betrayal, only to reveal later that he can still see but in a whole new way.

The Oracle smokes 'DOUBLE DESTINY' brand cigarettes.

According to John Milton's poem "Paradise Lost," Satan was once a very powerful angel named Lucifer until his pride got the best of him and he tried to take God's throne. A war raged in heaven, and Lucifer was cast down to the earth as Satan. Agent Smith was once a powerful agent who served the source (Deus ex Machina, God) until he chose to fight the system.

One of the bouncers at Club Hell calls Seraph "Wingless." A seraph is an angel with 6 wings, mentioned biblically in Isaiah 6.

Another derivitive Bible reference. Neo and Trinity go to the Machine City in the ship Logos. In Greek, "logos" means "word." So, Neo (Jesus), is going to deliver peace with "the word."

The ending of Neo is remarkably similar to the end of King Arthur in the Arthurian Legends. Arthur killed Mordred, leader of the army that was tearing apart Arthur's kingdom, in a one on one fight, but was mortally wounded. He was then borne on a barge to the "Isle of Avalon" to be healed. It also says that he would 'sleep until he was needed again'. Neo is "mortally wounded" (has his 'self' nearly destroyed) in the one on one battle with Smith, the leader of the army that is tearing apart the Matrix, and ends up being borne away, with us not truly knowing if he is alive or dead, to be 'healed' of his wound. The Oracle/Sati also says that they "might someday see him again".