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After Niobe/Ghost sees the oracle, agent smith comes out and says that he is the alfa of there omega, he is the beginning of there end.
I thought that was a pretty cool line, but look what i found
Revelation 1:8 I am Alpha and Omega, the beginning and the ending, saith the Lord, which is, and which was, and which is to come, the Almighty.
What could this mean?
Why would Smith Say something that was said by the lord?
Any ideas?

Smith wants all power. So he could rule. It just a good way to say I am the ultimate. He basically is insane and thinks of himself as a God.

Insane.. I think not, a rebel program with a plan.. I think so. If you remember correctly in the movie he wants nothing more than to rid his presence of the human race. To be the Alpha of their Omega, that would only mean that he is out to infect everybody. To rid him of the stench of the human world.

Definately, the Human race is a virus and he is the cure (in his eyes), but he has taken on the form of what he hates most and what he describes in the 1st film. Everyone has a purpose.

Also, Smith says in the first movie:

I want to share with you a Revelation I have come across during my time here...

Which fits with the biblical reference. I posted this in a thread a while back.

What was that biblical reference?

I am the Alpha, of your Omega, the Beginning, of Your End!

We also have the licence plate on his Audi which he pulls up in at the beginning of Reloaded:

IS5416

Take a look at Isaiah Chapter 54, Verse 16

will do

And holy shit, you reply fast...LOL

I know