Some say that the second installment in the trilogy didn't live up to the first. Then again, some say that it deepened the world and mythology and is better than the original.
Whatever the case, we're going to break it down.
In Matrix Reloaded, Neo meets a program called the Architect, the creator of the Matrix, who explains that Neo must make a choice to either reboot the Matrix and pick survivors to repopulate the Zion, or refuse, causing the Matrix to crash and killing everyone connected to it.
Let's get all philosophical and shit way down the rabbit hole.