Upon second viewing of Matrix Reloaded, I thought perhaps Neo was still in the Matrix. How else could he of stopped the killer machines in midair? And the SysOps (the white haired man in the room) said it was interesting watching Neo’s thought process. How could he do that unless Neo was still in the Matrix?
But then why would the SysOp put a Trojan Horse, the bad guy lying next to Neo in the closing scene, into a program, Zion, that he wrote? But then Neo, and all Matrix visitors from Zion, surely put filters on the connections to prevent virus attacks.
Yes, I believe he is. But I think it (Zion) is a different matrix. But you have some flaws in your post.
He’s the Architect, not the SysOps (he could be, but I’ve never heard that name before).
Neo was in the original matrix when he was talking to the Architect. That’s how he could “watch” Neo’s thought processes.
The Architect didn’t put a Trojan Horse into Zion. Bane has been corrupted by Agent Smith, as seen near the beginning of the movie. Smith is the Trojan Horse.
My thought is that the Zion-Matrix was the one made by the computers to keep the humans from looking any deeper. Correcting their previous mistakes, so to speak. If the humans thought they’d escaped the Matrix, they wouldn’t look any deeper and realize they’re still in the Matrix. If the computers didn’t fight them, however, they would get suspicious. Neo really is The One, because he’ll help the people escape all the Matrices.