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I realize others have already given good answers to these, but I feel like answering a few of them myself.
Originally posted by whiteknight
1) What was Seraph's connection to the Merovingian? They obviously recognize each other in the club scene. This probably isn't a maj0r point but I wanna know darnit.
The Merovingian calls Seraph the 'prodigal son', but also calls him Judas. It seems clear that Seraph was once a subordinate of the Merovingian, but then turned against him for some reason.
Incidentally, Seraph is an interesting name. Maybe you all know it already, but I'll just say it for the sake of completeness.
Remember how the Oracle tells Neo that errant programs are all over the place in Reloaded? She says, "Every time you hear a story about a ghost, an angel, or aliens, it's the Matrix trying to assimilate some program doing something that it's not supposed to."
Well, a Seraph is one of the Seraphim, the highest choir of angels. Apparently Seraph is very much one of those errant programs himself...
2) If all programs are put in the Matrix for a purpose, what is or was the Merovingians purpose?
I think he was probably some program dealing with the traffic of information in and out of the program, who then made a life for himself there, when a better program was written to replace him.
3) In the subway station where Neo wakes up and talks to the little girl and her family, what was it that the father said was his purpose in the Matrix? It was something to do with regulating power or something but I missed it. Again not a major point but I'm curious. I knew in "Reloaded" I saw someone being escorted out of the restaurant just as Neo and co. are walking in and was curious what that was about.
Rama-Kandra did exactly what you suspect. And yes, he is indeed the one we just glimpse walking away from the Merovingian's table as Neo, Trinity, and Morpheus approach it in Reloaded. If you have the Reloaded DVD (as I do), you can even verify that Rama-Kandra is on the list of characters in the end titles. Other than that, we didn't learn much about him, though.
4) The little girl (Seti?) seems to have One-like powers at the end. Is she just another One in the cycle or is she something new? In the game, the Oracle talks about sacrificing her old shell to help two programs and their child. She says she did so because the child was important and one day would change both the real world and the Matrix world forever.
Sadly I haven't played 'Enter the Matrix', so I can't help you.
5) What do you think the Oracle represents? Is she God? Why does Smith call her "Mom" ?
She is a program written to supplement the Architect by exploring the human psyche to help find out why humans initially rejected the Matrix. Being second only to the Architect would make her a powerful program indeed, and the Architect even says in 'Reloaded' that if he is the father, then she would undoubtedly be its mother. That could explain Smith's comment. But it might also be that Smith was originally written by the Oracle, though there is no information to further support that.
6) Who is the Arcitect? Is he just a reprsentation of the machine thing that Neo talks to at the end?
He is the program that created the Matrix. I don't think he is the same as the 'machine thing' Neo talks to, but he might have been created by it - he certainly is important enough that that might be the case.
7) Smith's little deja vu thing at the end suggests that all this has happened exactly this way before. Has every previous version of the Matrix ended this same way?
Don't forget that Smith is multiplying by copying himself onto other programs and human minds in the Matrix. That is why *everyone* in the Matrix is Smith during the final confrontation. The individual Smith that Neo is fighting is the Oracle. Note at the end when Smith and Neo are in the crater alone and they both 'explode'. After that the Oracle is suddenly lying there alone. Clearly she was the version of Smith that Neo was fighting, and when so when he had his deja vu, he was unwittingly using the Oracle's power to see the future. This might have been because he was seeing through her eyes at Neo. Note how the Merovingian is interested in obtaining the eyes of the Oracle. There is a point there, though it is sadly not explored much.
"We think we've come so far... Torture of heretics, burning of witches - it's all ancient history. Then, before you can blink an eye, suddenly it threatens to start all over again..."
- Captain Picard, "The Drumhead" (TNG).