Smith not only survived his own deletion at the end of M3, when version 6.1 of the Matrix is rebuilt to version 7.0, but evidently, the Analyst deliberately preserved either Smith or Agent Smith in the Matrix:
Smith not only survived his own deletion at the end of M3, when version 6.1 of the Matrix is rebuilt to version 7.0, but evidently, the Analyst deliberately preserved either Smith or Agent Smith in the Matrix:
Smith: You never appreciated our relationship. Not like The Analyst. Morpheus: The what? Neo: My doctor. Smith: He used our bond and turned it into a chain. It’s so obvious once you see it, right? But this whole altered-code update really blew my mind. I still don’t know how he did it. You, as a balding nerd. Hilarious. And me... even more perfect. Maybe a little too far on the piercing blue eyes. What do you think? |
However, doing something deliberately is not the same as having a desire to do it. Most likely, Smith's "special relationship" with Neo comes from the fact that Neo and Smith are logical opposites - one cannot exist without the other:
Oracle: He [Smith] is you. Your opposite, your negative. The result of the equation trying to balance itself out. (M3) |
Since Smith from Matrix version 6.1 had a special "connection" with Neo, the Analyst was most likely forced to put Smith into the simulation with Neo, suppressing Smith's code, which explains the Analyst's astonishment when the code is no longer suppressed:
Smith: Lies, lies and more lies. Analyst: Smith? Smith: What has the world come to when you can’t even trust a program? Analyst: How... Smith: Tom and I have more in common than you know. Once he got out, let’s just say, I was free to be me. |
| Back to Smith |
 Smith: Smith's Defeat |
 Smith: Analyst's Prison |