Odd... the Master didn't actually order them to self-destruct. They did it willingly, to amuse him.
Except, in the end, it didn't amuse him at all. When said why they were doing it, it took him by surprise, and he collapsed on his knees after it was over. I think he really cared about them. Also, it seems that the Master of Synapse can never sleep, or rest, so I'm guessing that drove him insane.
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