I can only recall two examples where we see the Matrix entirely in code (or rather, when it shows Neo viewing the Matrix as code, as I believe he's the only one who can do this).
Those two examples are after Neo gets up after being "killed" in the first film, and when we see Seraph's code when Neo first meets him in The Matrix: Reloaded.
Those are the only two instances I can think of where we see the Matrix all in code; are there any more? This isn't just restricted to the films; examples from the Animatrix, video games and official comics are also welcome (basically any official canon source).
Note that I'm only interested in instances that occur within the Matrix; so any examples within Construct programs or examples of Neo seeing gold code outside the Matrix in The Matrix: Revolutions don't count.
Also, I'm only looking for instances of when you see everything in code, not just partially in code; an example of something that doesn't count is when we see Sati and the cat after the Matrix is reset at the end of Revolutions, where we kinda see a bit of green code as the Matrix being is restored, just before the cat goes up to Sati (see the gif in this answer).