Spoiler alert!
Movie starts out boring so a lot of people will lose interest but is well worth the wait.
This movie shows the evolution of the machines and how they went from simple organisms looking just to survive and using humans as batteries to eventually betraying their own kind and rebelling against each other.
The machines actually take sides and some ally with the humans to make a new world. Trinity and Neo are cloned since the machines "The analyst" realizes that humans make more power when feelings are programmed into the matrix, humans are no longer just there living to provide power but the machines figure that the algorithm requires more than just a world to contain the humas...excellent movie!
Oh yeah and the reason Morpheus is not there is because he wasn't cloned, he died long ago. The "Good machines" made a virtual clone of Morpheus to find and pull the cloned Neo out of the Matrix just like the original movie...so much more to this movie but just watch!