I thought all of Zion died. Remember, the guys in the ship that escaped said that it was a massacre. Were they just talking about their own ships? If so, why weren't they heading back in to defend Zion?
The captain of the ship that picked up the crew of the Nebuchadnezzar said that the ships sent into the access tunnels to ambush the Sentinels had been massacred because one of the ships set off an EMP prematurely. The only survivor of this massacre was Bane, who had been "possessed" by Agent Smith in the Matrix.
Of course, we all know that Zion REALLLLY doesn't exist anymore because it NEVER existed. It was part of the second Matrix created to contain that small percentage of people who rejected the first Matrix. Right?
Maybe so.