IMO the apple was just a peace offering. They decided to bring something that was significant that was organic and couldn't really be built by them and, since Zero One was created in the cradle of civilization and where human life,( according to the Christian bible)was created they sent an Adam and Eve as delegates and an apple as a peace offering. Well since the humans didn't agree to be peaceful and work with the robots, like the robots had asked for, the rotting of the apple signifies that we were given a chance at something, but we most likely killed the Zero One delegates and then resorted to violence and a chance at peace rotted away. The second apple, the one the machine is holding in the courtroom after the war, shows that they now have the upper hand, they gave us this chance and we pissed it away, and they still have the power to give it to use again but they are keeping this one, so it places the apple on the desk and keeps it there.
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