During the first encounter with Agent Smith, Neo is not in #TheMatrix during the interrogation. He's in a side-server or a virtual machine where the Agents have more control than they do in The Matrix proper. That's why they could remove his mouth, etc, there, but not normally
#matrixmovies — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #matrixmovies, aggregated by home.social.
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When #Bane was infected with #SmithVirus, the #SmithBane cut himself because Bane was still in there, trying to stop Smith, trying to cut Smith out of his body
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There was never a war with the machines. The machines were always working to preserve humanity in the best way they could. (Humans fucked up the ecosystem by being humans.)
That's why the first #matrix was a paradise. The machines only invented "the war" to keep the humans from killing themselves in paradise.