Edit2: probably solved. I didn’t understand that Brown is talking about Neo and Trinity’s attack.
Agent Smith is questioning Morpheus, trying to extract the codes to the Zion mainframe. Neo and Trinity have attacked the building in which Morpheus is being held, trying to save him.
(Office)
Agent Jones: What were you doing?
Agent Brown: He doesn’t know.
Agent Smith: Know what?
It feels too poignant to have a machine say this without there being something else to it.
Edit: what I mean is, a machine wouldn’t “retort” or be passive aggressive like this.


I, too, originally took the line to mean that Smith didn’t know what he was doing, like he was out of his mind, which played into the deranged speech he’d just given. Turns out I was reading way too far into it.
Phew, I wasn’t the only one then 😅