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.
What perplexes me is why the piece of software disconnects itself in order to interrogate morphus and confess his feelings. It’s really agent smith that is ‘the one’, undergoing the epiphany, a bit of software that has become sentient (or at least homo) enough to have shame and anger, and seek independence. Which is, of course, impossible.