At the start has a line "we've been watching you"
They take him to another world, like the watcher's world.
Then when get him the teach him heaps of stuff with the computer plugged into him. the dude that teaches neo all the stuff was born outside of the matrix, like the watchers.
He is Gadreel (or Gader'el) taught the art of cosmetics, the use of weapons and killing blows.
Cosmetics is the bit where they have the loading area where they can change their clothes,
Then they teach him kung fu.
The agents are archons.
archons rule this fake world to feed off our pain. (adrenochrome)
agents rule the matrix (fake world) created to feed off our body heat.
Agent Smith: Did you know that the first Matrix was designed to be a perfect human world? Where none suffered, where everyone would be happy. It was a disaster. No one would accept the program. Entire crops were lost.
Archons like biblical angles cannot create, its something humans can do.
Agent Smith: You move to an area and you multiply and multiply until every natural resource is consumed and the only way you can survive is to spread to another area.
The ship in the matrix is called the Nebuchadnezzar. Nebuchadnezzar was a king that had a dream about watchers, the ship is where they dream of the matrix.
Watchers are also called Grigori translates to "waking", "awake". matrix has bits about awaking from the matrix.
Neo’s passport was issued on the 12th of September 1991 and will expire on the 11th of September 2001.