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I dont know whether this has been asked earlier on but i was under the impression that you need an operator to jack you into the matrix...
So in M1 how does cypher jack himself into the matrix to meet smith... and why doesnt anyone (morpheus, trinity tank etc) see where he is and what he is up to and pull the plug from him?
Or is this just another hole in the movie

Remember when neo talks to cypher a bit earlier in the film? It is then that cypher is automatically setting up a program to jack in later {or so people say}. As to why no one noticed, maybe Cypher said to the group that he wanted a little alone time with the woman in red...

but wouldnt mouse have to set that up with him?

no...remember...most of the people, if not all of them, that are jacked out, are hackers...they know how to write code, and they can do simple porgrams like automated phone pickup and routing...

To me, it's just one of a few dozen "unanswered questions" regarding the Matrix Trilogy.

.... meaning it's left open for matrix geeks to 'hack it out'.