She wasn't in the game she was in the loop that Neo created, which would be similar to the construct that they use for training and loading things they need. If you remember in the first movie Neo was hurt after using the construct for his fight with Morpheus so the life and death rules applied.You know, the more I think about this the more confused I get.
In the opening scenes, the Resistance members are in the "game" world, but they have to "break" out of it just like breaking out of the Matrix. BUT...since they are just actually playing a game while inside of the new Matrix, then why do they have to break out of it? If you die in the Matrix you die for real, but if you die in a game you don't die for real. So, unless Neo's game is so real that it kills you, there should be no reason for the Resistance members to worry about anything that happens inside of a game. The "agents" inside the game are not real agents, they're just NPCs. They should be able to just quit the game like any other Matrix inhabitant would be able to do.
Yeah, the end of the first movie should have probably been the end point of "The One's" story.
Neo basically ascended to digital Godhood, then right back at the beginning of Matrix 2 he's back to running from "upgraded" Agents.
Once you are no longer bound by the rules of the Matrix, nothing in the Matrix should have been able to touch Neo at all.
He wasn't running from upgraded agents. He kicked their asses and then left to look for the Oracle.