This is a possibly the best sci-fi movie of all time. Everything in it is great and beyond comparison and the only thing few people have against it is the complexity in its plot.
Reloaded gives the foundation for Revolutions. The architect scene is the most critical scene in the entire trilogy. The Architect presents Neo with a choice, but he emphasizes that the choice is barely a choice at all. This is not only true for the humans but also for machines. So, unless Neo chooses the door that integrates him with the Source the machines face destruction because of Smith that is seen in Revolutions.
This is also a theme behind Revolutions is the machines do not want war any more than the humans do, but, the war with the humans is a cause of their inability to understand humans. But Smith proliferates & is beyond control. Neo Lets himself get infected where by Smith has no purpose to serve & is killed.
The humans & machines strike a deal of peace. Obviously the Matrix is reconstructed to early 20h century. The only change being those who become aware of the choice shall be freed. It is more as a compromise & justice being served.