The third Matrix movie has the least philosophy of all three Matrix movies. There are certain quasi-religious references and themes, but these are superficial and do not connect well with the themes and philosophical musings of the first two movies, leaving questions about the meaning of ideas raised on those movies. The third movie does not seem to be a completion of the first two; instead, it almost seems to be a separate movie.
The theme of love is strong. At the very beginning, Neo, the hero, meets a little girl and her parents. It turns out that they are programs, but the father says that he loves his little girl and so they are leaving the Matrix. Neo is confused since computer programs are not supposed to have emotions like love. When the Oracle (who takes the form of an older woman) is baking cookies with the same little girl, she tells her that cookies must be made with love. Later, the woman Zee decides to stay around in Zion for a dangerous battle situation because she wants to be there when the man she loves arrives in a ship. Finally, Trinity states that she is willing to die for Neo, and she does eventually die while taking Neo to the machines where he believes he needs to go to make peace. Agent Smith, the villain, in his fight with Neo at the end, makes fun of love, peace, justice, and other ideals, saying that they have no meaning or reality. The end of the movie has the same little girl from the beginning, and she seems to represent innocence and love. Possibly, the message is that only humans can love, yet we are told at the beginning that the computer programs can learn to love, which is somewhat confusing if we are to believe machines and humans are different in that only humans can love. Is the message that machines can learn to love? If so, what does this mean? This theme is so weak and unexplored that it is merely superficial and meaningless.
Not much mystery from the first two movies is solved in this movie. The Oracle tells Neo that Agent Smith is his opposite -- Neo's "negative." She also tells Neo that the Architect's purpose (the Architect appears at the end of the second movie in a very enigmatic role) is to balance equations and her purpose is to disrupt or unbalance them. What does this suggest? That for every action there is a reaction? Or that where there is order, there must be disorder? Along with Agent Smith being Neo's "negative," this almost suggests a yin/yang view that everything must have an opposite to exist, but this idea is not followed through. There is no clue given about why things are this way, if they will continue to be this way, or how this connects with other events in the movie.
Neo fights Agent Smith and after being turned into an Agent Smith look-alike, Neo suddenly radiates light and turns back into himself, destroying all the Agent Smith clones and Agent Smith himself. The movie does not explain how or why Neo can do this. One wonders why he did not do this before. One scene shows the radiating Neo with his arms out in a Christlike posture, obviously implying Neo is a type of Christ or Savior, something alluded to in the earlier movies, but it has little meaning as we don't know what it cost Neo to do this (other than losing Trinity). It is not even clear that he is suffering. If he did this by a mere special ability, then what is admirable here? His fight with Agent Smith was similar to other fights in the previous movies. Agent Smith's "death" is very anticlimactic, as is Neo's victory. It is not clear if Neo lives or not, but at the end when the little girl asks the Oracle (who had been deleted by Agent Smith but has now returned) if Neo will be back, the Oracle answers along the lines of, "I am sure he will be back someday." Somehow, we don't care much by this point whether Neo is alive or not.
At two points in the movie, characters say, "I believe." One is said by a young fighter in Zion as he opens a gate to let in a ship that will fight the machines. The Oracle also says, "I believe" at the end. But it is unclear as to what it is they are believing in . Do they believe in Neo? That Neo is "the One?" In victory? In the human spirit? In peace? It is fine for movies to raise thought provoking questions, but this statement about belief is merely confusing and seems thrown in for no reason and with no connection to anything else.
The issues of illusion and reality, so strongly present in the first two movies, are absent in this one. This movie is more like a fighting movie and the philosophical threads from the first two movies are left lying helplessly on the floor.