Now Zivan, remember the 'system failure' at the end of the first matrix? I believe that is what the architect was talking about.
oh shit.. no!! matrix again!
When Neo became "The One," the matrix began to break down. That's why the rebels freed more people in the last 6 months than they had in the prior 6 years.
errr... ok.. stop.
That is why the architect said that if Neo didn't rejoin the Matrix and disperse his code to the new matrix, everything and everyone would die.