Contrary to popular belief, neither Agent Brown nor Agent Jones fled from fear.
Machines do not feel fear like men do.
Machines have maths. Know how to survive.
Neo fought Smith and broke his body. But was more than that.
The world had rules, he broke them and made an internal change in Smith. Code rewrote from inside out.
A loss of host body.
This is an unimportant thing for the Agent.
The Agents just transfer to another man on the street.
This is what Neo has done to him – he deleted the Agent.
True deletion.
Matrix is a dark business. A corrupt program has two ways - other than go back to the Source and be erased, it must hide.
It was clear for Brown and Jones that Neo had the key code.
The fight was lost. If they stayed, their own code would be ruined, ended forever.