I've read on a few forums people saying things along the lines of, "Matriculated was my least favourite of the Animatrix anime, but then I watched it a few times and realised what was going on. Now it's my favourite."
I just watched it for the first time and, try as I did, I could not figure out what was going on. It seems the humans are attempting to "convert" an enemy AI to their side using a simulation. It's not explained precisely what they're doing in order to persuade it, but it seems to work.
Then the crew are attacked in real life (thanks to the beacon that was dropped by the AI), and the AI saves a crew member. Once its done this, however, it tries to re-enter the simulation with the crew member -- apparently being aware that it was in a simulation afterall -- but the human crew-member freaks out (and dies?).
What did I miss?