Shadow looked at Yami, as she was able to earn his consent to act, by means of helping Mokuba see reason, and perhaps get him to calm down, and think about what he was doing. Turning back to Mokuba, she looked into his eyes, the genie's red ones started to slightly glow, having to gaze into his very soul; something that Mokuba would be able to feel, as if she was passing within his very body. Even though she wasn't literally doing so, Shadow was reaching out towards the shadow part of his very being. [i]'I know you can hear me, child'[/i], her voice going to him in a whisper. Even though he can't see her, the boy can most-definitely hear her. 

[i]'I know that your brother is most-important to you. As his fellow kin, you would do anything for him. But you must see the bigger picture, Mokuba Kaiba. Pegasus is not what he seems and, even though your gut says for you to take him head-on, your heart can't reach Seto through theft and sabotage. Your life is just as in danger, as is your brother. Please, allow Yugi to help you. Allow us to help you. Pegasus can’t take us all, at once'[/i]. 

Her persuasion power was in effect, after tapping into the boy's shadow-half. Eventually, she managed to let Mokuba go from her supernaturally-piercing gaze, allowing him to finally let out a breath.