Shadow has been living in Yugi's shadow for the past ten months after his wish for her freedom, and the opportunity to not (forcefully) grant wishes anymore was a new chance. She had to admit that the task itself was very difficult; to obey at all times, and not oppose or judge the decisions made by the master. From her past life, and for learning the cons of her servitude, Shadow admitted that she got a little carried away with her dream to become like Divine. She didn't know about the stress, or the tiredness that her sister suffered from while performing the said-task, and it was not what the shadow genie wanted to expect at all. Not to mention that this lesson was learned after Bakura and Marik used her loyal nature against her will, in order to get close to Yugi. 

Except, in Bakura's case, he only wanted her power in general; his only reason to take control of her in the first place. From there, Shadow Djinn was devoted to use her shadows for the greater good: to track and monitor the shades of the living, eliminating all anomalies lurking within the darkness of their hearts, or "shadows", for that matter. Her insecurity to even vouch for humans was beyond her reach, since she was, in fact, unseeable. Except to those who possesses the ability to see the "spirits" in the first place i.e. Yugi, Pegasus, Jaden, Jesse, Yusei, and Yuya. However, this "invisibility" wasn't to last; thanks to the Syncro-Duelist Yusei Fudo, she had the choice whether to be noticeable [i]or[/i] unnoticeable to [b]everyone[/b]. 

All of them were her friends; all were human; all were allies; only one was a spirit: Yubel. For the past ten months, she missed communicating with Jaden's spirit partner. Speaking of, Shadow honestly missed Pharaoh; he showed her the courage she should've possessed, and for the scenario of both of them traveling five-thousand years into the past, it slowly emerged within her, when he frequently reminded her that she was a shadow-being; that she had the free-will to choose, whether to follow the rules or not. That was the only thing that was holding her back: self-awareness. Shadow went through these said memories, when she secured herself within Yugi's shadow as he walked through Domino City's park. Not that she complained; she talked to him through his own casted shadow on the ground as he walked, moving on its own. 

However, their communication came to a halt when someone bumped into her owner, causing Shadow to disappear. Seeing that it was just her old friend Jaden Yuki, she was tempted to say 'hello', but once she witnessed Yugi passing her card off to him, she wanted to protest in confusion. However, with his request, she couldn't deny his "wish". He was her friend, and she didn't want to see him disappointed if she refused. But once she realized herself being one with her card, she was to temporarily be with duelist after duelist. This was a new chapter, and with that, the Shadow Genie's confidence came back. 'I promise', she responded to the boy, missing him already once Jaden made his run. It was time to move on, but who knows when their paths might cross again?

~Kaiba Corp Dueling Arena~
[i]'Yeah, Jay, everyone's dying here. Must be a very popular place in Domino'[/i], Shadow pointed out, also revealing her transparent self on Jaden's other side, in her natural form, just opposite of Yubel. Watching the duelists before them, she remembered Yugi giving her his deck before she went back into his card. He wanted her to keep them, in memory of Atem. In return, Shadow traded with him her sister's card, and she was happy that Divine was able to go to a better place in the Shrine, along with the Pharaoh. It left a fonding memory behind, and that was one to keep. The genie looked at her new owner, before switching her appearance to her disguised form, and switching on the specially-designed bracelet Yusei made for her, making herself, well, noticeable. Slightly taller than Jaden, while holding the deck in her hand, a Duel Disk appeared on her left arm. Hopefully no one recognizes her as the Queen of Games in her. "Let's get into that school", Shadow said with a confident smile.