Ummm, after Neo left the Architect guy and headed back into the Matrix to save Trinity - Why was the building exploding as he flew out of it? Did they cut a scene out? And what happened to Morpheus? Was he not just outside the door of light when the building went up?
The Keymaker opened a door "home", either to a hardline location or directly back to the Neb, just before he died.
I believe the explosives wired to the building exploded after the 314 second window expired - per the Keymaker, this was the time that Neo had to contact the Source after the other Zionites shut down the power before the power was restored.