Kaiba paying his respect to Kisara
Kaiba had seen how the Blue-Eyes came to be his. It hadn’t been done with forceful means like he did with the BEWD cards in the manga and anime, but out of love, devotion, and a desire to protect (from a corrupted father figure).
Did he see at that moment their similarity in the length they would go to for their most important person, showing why said dragon is his most beautiful and most loyal servant (shimobe), and the embodiment of his pride and soul? Just for that (if not, then as the first owner of the dragon), she deserves his respect and gratitude.
I like to believe he lowered his head to express those two things to her. I also noticed his eyes blinked rapidly for a split second after that, indicating he’s struggling emotionally and / or lying. My guess is both: Kaiba may scoff at the occult and the past (lying), but we know they affect him more than he lets on (struggling emotionally). In other words, he had finally acknowledged the 3000 yearlong connection he shared with Kisara.
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