The major themes of the movie are freedom and learning about and embracing the truth. There are only a few humans in the world that are free from the Matrix; these are the ones that are aware of the truth of the real world and the Matrix and have chosen to accept these truths. Furthermore, another aspect of freedom involves the fight that Neo and his crew face when it comes to the agents of the Matrix, which are the programs that ensure that everything is running smoothly within this cyberworld. This also leads into part of the central conflicts of the film.
There are two central conflicts in the film: Neo versus Agent Smith, and the humans versus the machines. Agent Smith, who is about as free from the Matrix as the sleeping humans are, is against the fact that Neo understands the truth about the Matrix. Smith does not like the enemy he has found in Neo. The humans versus the machines is the original conflict, something that began before the start of the movie. The purpose of this fight is to make sure that as few humans as possible know about the Matrix setup. As it is, the humans that do know is too many for comfort to the machines. The freed humans, however, feel that it is their duty to make aware as many sleeping humans that they can. Unfortunately, part of this battle involves keeping away from the curious machines as much as possible - an impossible feat.
These tensions are not resolved. By the end of the film, the two separate battles are still raging. Neo does temporarily defeat Agent Smith, but the other agents are ready to take on the task of bringing down the free humans. The war between humans and machines continue on.
One of the main things that kept coming up throughout the film is the obvious differences between the real world and the Matrix; the physical reality and the computerized mockery of life. Furthermore, there are many religious,