On numerous occasions, we see the Agents moving in and out of people who're still hardwired to the Matrix. They appear to see what they see (as evidenced by the [Vagrant in the subway](http://youtu.be/7GSgWzmR_-c?t=9s) who sees the team jacking out) and can move in and out of them with no apparent difficulty.

They physically manipulate Neo by changing his self-image to remove his mouth and then implant a bug in him. 

**What did the [bug](http://matrix.wikia.com/wiki/Bug) do and why was it needed if the Agents can *already see what bluepills can see?***

![enter image description here](https://i.stack.imgur.com/zJvkc.jpg)