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I have seen the Matrix movies over and over almost knowing every word off by heart. But the one thing that perplexes me is why the Agents (Smith etc) once they captured Morpheus, not send in more Agents to protect him from being rescued by Neo and Trinity? They must have known Neo would have tried to rescue him.
Besides, Neo is "part" of the puzzle to balance the Matrix right? So killing Neo is out of the question. I believe Agent Smith could have done that from the first movie when they fought in the subway - if he was allowed to (he was still connected to the machines). Smith simply has the skills preprogrammed into him by the machines. Neo only recently had the training given to him.
I am convinced that they needed Neo to fulfill the "prophecy" but they could not kill Morpheus just yet, or at least until Neo has completed his mission to bring order back into The Matrix. This is why they only used "loose" security around Morpheus. Otherwise they would have killed him the moment they captured him.
Furthermore, I also think they wanted Morpheus to gain access to another machine or machine world. I suspect the hard-drives in Zion were the keys to those other 'worlds'. The movies were set in a time when machines were at war with other machines, I think. Zion and humans were like hippies, more a distraction than a threat. But Morpheus, he was numero uno! He had the access codes, the knowledge, etc everything into the 'other' machines or another Matrix if you will.
I do not believe they wanted the codes to break into Zion itself, as they've done that 'very well in the past ... Many times'. So my question is, if Morpheus was THAT important to the machines, then why only the weak security once captured? And I do not believe they were over resourced. Come on, the machines can turn any "human" into an Agent.