[Chango]

Just to clear one thing up, Zion is not destroyed, the machines haven't reached it yet. In the scene after Neo and Trinity left the matrix and he told Morpheus that the prophecy is false he said that "Zion will be destroyed in 24 hours if we don't do anything." And the slaughter that the captain of the ship that rescued Neo, Trinity, Morpheus and Link was referring to was a counter-attack at the machines at one of the areas the commander was talking about earlier in the film (the one in front of the council.) 5 ships were sent to attack the machines and whatever one Cain (the guy that was infected by Agent Smith) was on set off its EMP early and disabled 3 other ships and they were all slaughtered except for Cain, who was rescued.