Corrected entry: Tank explains to Neo and Trinity that the reason the agents took Morpheus is because all captains to the ships are given codes to access Zion's mainframe and if an agent gets into the system it could destroy them. In the Matrix: Reloaded though, the Architect tells Neo "This is the sixth time we have destroyed it and we have become quite exceeding at it." Talking about Zion. If the machines have successfully destroyed it in the past six times, why would the agents need to even get into the computer to destroy them when they would just do it later?
Phixius
17th Oct 2010
Correction: As the Architect stated, they've gotten better and better at destroying Zion. This is just another attempt to continue improving and become even more efficient.
Phixius ★