They are scanning his memories. His duel disk was rigged so that if he ever tried to use his full power, he would be brought back to Academia.
When he got back, they acknowledged that it wasn’t a “standard” duelist that caused this. So they are scanning his memories entirely. This also means they are going to learn about Pendulums and Reiji’s tournament. (and Shun being weaseled in)
This is also why Reiji asked for his duel disk before. He was aware something was up with it and probably figured out it would call him back if he ever tried to use his power.
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