Shadow watched as Yugi steeled himself together to work up his courage. [i]That's the spirit[/i], she thought with satisfaction, before she faded away from next to him. The genie tempted to chuckle at the scene between her master and Joey. [i]Yugi must be [i]that[/i] pure[/i], after all, she concluded. Her predictions were true about this boy; he had this "friendly" element, and she could sense through his shadow that radiated a lot of positive energy, although there was a slight chip of timidness attached to it. But she figured that that was just a natural addition to his being. 

Once he and Joey hit the rails upon the vessel, she came back out again, standing at Yugi's opposite side, while the blonde teen was on the other.