Given that the dude spends plenty of time jacked into the Matrix, at risk of being captured by the Agents, why does he have access codes to Zion mainframe in his head?
Why aren't they on some flash drive activated by his brainwaves/voice print/iris scan etc... safely offline from the matrix?
The first movie made a point of showing that the machines couldn't just hack some poor slob's brain. Smith spends considerable time and energy trying to torture the information out of Morpheus.
A hard-copy can be accessed with enough time and energy. It's a physical device the Machines could work on. As is, if Morpheus dies, the codes die with him. That's pretty secure.
But in the end it was all moot, since they just knocked down a wall.
Given the example of Cypher, I would argue that physical stored access codes would not be necessarily more secure. A biometrically protected device is only as good as no one's using physical force to show your eye, finger, etc, to the scanner, and a safe itself can still be stolen and broken into manually. Keep the codes in his head means he is at the same risk of being captured, but the device itself cannot be stolen.
Always remember that the Matrix is a visualization only - it's not real. When Smith tortures Morpheus, we see Morpheus sweat but he doesn't sweat on board of his ship. It's just a visualization of him struggling against the attack.
So when they say "codes", that doesn't necessarily mean a pin code. It can mean an idea or an image which Morpheus has to think in his real brain which the "mainframe" (which probably doesn't look like anything we'd recognize) accepts. It could be a blue elephant. In this scenario, Smith tells Morpheus "think of a blue elephant" so his probes can copy the "code" and Morpheus tries to avoid just that.
Maybe the agents try to copy important memories from Morpheus which the mainframe will recognize. That could be a couple of sentences which they told each other or some event they shared.
That said, the "reality" in which Zion "exists" might be just another level of the Matrix. I don't know whether Morpheus is aware of this (in the theory, Neo is but only when the Architect tells him). In this scenario, the access codes are purely virtual as is Zion, the ship, the farm in which Neo wakes up, the devastated surface of the earth, everything - the actors never really wake up.
If you think about it from this angle, then all the information which we have is pretty shaky: If a body can never be removed from the real Matrix, then the connectors could be looking completely different. Maybe Neo and the others are just brains floating in jars.
The more interesting question here is probably: If Morpheus never really left the Matrix, why do the machines have to bother to get the codes from him?
If this is true, the "codes" are just a hoax to keep the humans in Zion occupied.
Because its the most secure and reliable way to store the codes
Here's why:
All very good reasons not to physically store the code: And here's why its a very good idea to memorize it instead. If captured in the matrix the crew has options
So in conclusion, its is the best and safest way. This assumes that there must be a reason why a ships captain has to know the code. The only reason this scene makes it look like a huge security weakness is because of the dilemma, the crew don't want to kill him. Other than that it isn't a problem and is very secure. If he did reveal the codes the crew could still unplug him, fly FAST to get in range of Zion and warn them. Any other method of storage could allow the machines to get the code without anyone noticing!
Also one last thing. The machines don't want to destroy Zion yet anyway, so they don't need the code. Its more likely the Agents weren't aware of the Architect plans, or were working towards it by their actions somehow. Read this for more on this plan
Suppose they keep it on a pendrive instead... How long would it take for a traitor to copy the pendrive image, give it to the agents and wait until the Machine Mainframe cracks the encryption?
I'm a bit late to this party, but interesting to read the responses to this.
The codes did not matter, they are merely the Maguffin that propels the story (agents chase Morpheous etc, agents capture Morpheous, Neo comes to rescue etc).
The machines had no need of codes, they are merely playing their part in the program to bring about THE ONE so they can start their attack on Zion (as they have done 5 times previously).
When Neo becomes THE ONE, the machines don't follow the people back to Zion to locate it, they launch an army of big digging machines to drill straight down and past Zion's defences (implying they knew where it was all along and how to bypass the defences). As the architect says they have attacked Zion and the ONE 5 times before and are efficient at it.
The old tech driving Zion shows that it remains between "rounds" of the resistance/ONE game. Once attacked the ONE and the 7 men/16 women go to the source, no doubt to return later (probably years) as part of the program of control.
The codes are there to give the agents/rebels something to do whilst they await the discovery of THE ONE.
This is, in my opinion the biggest plot hole in the whole movie. Not only was it unnecessary for him to have the codes memorised, I take this a step further.
When Morpheus is captured the rest of the crew gets ready to unplug him before he could reveal the codes. But think about it... does it really matter if the agents get access to the codes? If the code is leaked to the machines, simply change them on the mainframe.
Unless the access codes are somehow "hardcoded" into the mainframe (which would be an incredibly stupid design) you can simply change them as necessary.
