Well with the fibre install down the road leading to the phone/dsl line being cut accidentally, I ended up watching the trilogy again during the downtime, and while it unfortunately led to more plot holes becoming apparent, the part about Neo being partially a program got me thinking, along with something else I noticed.
Is Trinity part, if not entirely a program as well? She's able to hack the IRS database, something that's next to impossible apparently, which just so happens to give her legendary status among the hacker community, which Neo is a part of, that allows him to relate to her in a more personal manner. There's no way that doesn't play into his attraction for her, and look at how she keeps him alive, and seems to be there for him when he needs her most, like when she somehow is able to blow the agents head off on the roof to save Neo, when nobody has ever defeated an agent, other than Neo, eventually.
As Neo goes through the trilogy, the programs become more open and up front with him, flat out telling him they have a purpose, and even when they die they say things like, 'it was meant to be', because they know. When Trinity finally dies, she says, "its ok, it's time", as if she knows she's fulfilled her purpose like the other programs. If Smith can become partially a human, and Neo is partially a program, why couldn't Trinity be?
There is also the scene in the 'real world' where Smith (Bane) has a knife to Trinity's throat and after getting Neo to drop his weapon and back off, instead of taking Trinity out and rushing for the gun, he throws her down the hatch instead. This seems like a really dumb move because what is the point in keeping her alive? It's just another potential threat to deal with after he's taken out Neo. He even tells her how satisfying it will be to kill both of them. However, if part of Smith's programming purpose is not to kill Trinity though, then that would make sense, especially since he also mentions to her, 'all the times you got away from me'. Trinity would need to be able to finish her purpose, in getting Neo to the source, and Smith killing her would interfere with that.
Then there's the point when she and Neo get above the clouds and see the sunset, where Trinity just says "beautiful", before descending back towards the machine city, where she finally bites the dust. Doesn't it seem coincidental, that Sati, the child program, with no purpose and born from love, something programs apparently don't understand, creates a sunset at the rebirth of The Matrix, reminiscent of what Trinity and Neo saw not all that long ago in the 'real world'? When Sati points it out to the Oracle, her response is exactly the same as Trinity's, "beautiful", just by chance.
It's as if both Neo's and Trinity's experiences, even in the real world, are being taken into account and sometimes incorporated into The Matrix, and possibly for good reason.
So what's the point of all that? What if the prophecy really is BS in the way in which the humans understand it? What if the Oracle is overall, helping the machines, but also helping the humans somewhat as a consequence? What if the point of The Matrix, from the start, before the trilogy, was to create the perfect system that would assure the humans would remain asleep in the real world? One where everything they would've experienced in the real world from the past, can and will happen within The Matrix now, considering it couldn't be that way before because the programs weren't entirely acting like humans, because they didn't understand them fully.
Imagine a Matrix where the machines now understand everything fully, including love. One where programs no longer are born with purpose, but free to choose and feel just like a human would. What are the odds of any humans waking up from this perfected version because they can sense something is wrong? Extremely unlikely, which would be the point. Figure out a way to stop the humans from waking up period. As for the humans, they basically get to live a 'real life', in terms of what they experience in this final perfected version of The Matrix, without actually having to physically live it, since it's all mental, while the machines get to keep using the humans. It's basically a win win situation in a way.
This would to some degree explain how Neo and Trinity can return in a sequel and have it make sense. If part of them or more is program, and their every thought and experience was being saved from before, then it's not hard to see how the machines could resurrect them. Neo or Trinity wouldn't need to exist in the real world either, since they could possibly be duplicated exactly how they were when they died, but as programs now.
Since nobody is waking up anymore because this final Matrix is so perfect, maybe the entire movie takes place within The Matrix? That would partially explain why they wouldn't need a Morpheus. Maybe the Zion survivors have to now hack into The Matrix again and convince Neo and Trinity that The Matrix is actually fake and to help end it for good somehow, since "The One" won't be emerging due to there being no reason for that to happen? Morpheus was still alive in Zion though, so unless they do something like place the time period well into the future after he's dead, when Zion has been rebuilt and they've been able to finally hack back into The Matrix, that might work.
