10 Famous Movie Plot Holes (That Are NOT Plot Holes)
9. How Did Cypher Enter The Matrix By Himself? - The Matrix
Morpheus and his crew have dedicated their lives to freeing as many minds as possible from The Matrix; a simulation that is indistinguishable from 21st century life. Morpheus explains to Neo that everyone has great difficulty adjusting when they are released from The Matrix as they realise their entire life was a lie.
One of Morpheus' crewmembers, Cypher, has grown tired of living in the real world and intends to go back to living in The Matrix. In one scene, we see him inside the Matrix, selling out his teammates to Agent Smith. This moment bothers a lot of people since it has been emphasised that a person cannot jack into The Matrix without a separate person serving as the operator
But according to the directors, Cypher isn't in The Matrix. He is in a separate program he constructed that allows him to jack in and out at will. He designed it so no one else can access it, except The Agents, so he can talk to them in private.
Although it's not made clear, the reason why Cypher acts so jumpy when Neo enters his quarters is because he's putting the final touches on this secret program before entering it.