At first, Yugi thought it was just the death of his Other Self- of Atem, he has to remember that- that was causing it. He felt empty inside, the world was out of focus, fuzzy, colorless and dull; but that was normal, right? Jonouchi, Honda and Anzu were all feeling the same things, especially Anzu. Surely it was just grief that gnawed at his heart and left this gaping hole that would never, ever be filled. And so he went on, as everyone else did. He was brave, smiled as best he could and tried to be normal.
A month passed, and then two. Honda was moving on with his life, and even seemed to have forgotten all about Atem sometimes, something Yugi couldn't imagine. Honda had found work part time at a mechanic, and they didn't see him often anymore. Yugi barely noticed.
Jonouchi was the next to come to terms with everything, six months after losing Atem. He dealt with it differently than Honda- rather than leave that part of his life behind all together; he had truly accepted that Atem was gone. That was even harder for Yugi to imagine. For a while Yugi avoided Jonouchi, but he couldn't stay away for long. Jonouchi was his best friend, and while hearing Atem's name still hurt, eventually it wasn't as painful as it once was, and Yugi was sure he was starting to heal.
Then, a year after Atem left, once they had all graduated and were making their way in the world, Anzu announced that she was seeing someone. Yugi's world crumbled. Anzu had been the only person who came close to loving Atem like he did. But now, she was dating. The last person who had shared in his mourning was getting over everything, and Yugi still felt broken inside.
Two years after Atem passed on, Yugi had an epiphany. In the dark, he wondered- perhaps when Atem had gone it ihad/i left a hole- a literal one through which the shadows were pouring, threatening to take over his very being. It was a scary thought, and so the next day he would laugh it off as a silly delusion, just his own fancy trying to explain away his inability to just get over it. But the hole remained and the darkness pulled insistently at his soul.
Six months later, Yugi meets up with Ryou Bakura on a dig in the Valley of the Kings. They smile at each other, plastic smiles, and Yugi notices that his friend doesn't look well. Bakura is ragged and there is an unnerving flatness to his eyes. Yugi can clearly see himself reflected in them, and realizes that he didn't look much better. Funny that he hadn't seen that this morning when he looked in the mirror. They agree to meet up for drinks later, and it is only when they part ways and the world dims once more that Yugi realizes it had brightened.
They meet up after work at a small cafe, and with Bakura, Yugi feels better than he has in a long time. The hole is still sucking away, but it becomes bearable while he's in the other's company. Bakura has perked up as well, some animation is back in his face and he seems truly happy to be with an old friend. They talk for a long time. Soon the cafe is closing, and Yugi doesn't want to leave the sanctuary of Ryou's presence, so he agrees readily to come back to Bakura's apartment and continue their chat.
When they get there, Ryou makes Yugi comfortable, and he just feels so good that it all comes spilling out, his late night worries and the terrifying depression. Yugi hasn't shared this with anyone, because until now even he thought he was just imagining things. But then Bakura speaks up quietly, and he tells Yugi that he's felt the same things. For a time they both bask in the glory of knowing that they aren't alone. But the glow fades quickly as they realize that they still have a problem, and that it won't be going away any time soon. It hurts.
Yugi isn't sure how it happens, but suddenly he and Ryou are kissing, lips locked in a sweet, desperate attempt at comfort. And, for a moment, they are Kings of the Shadows, ruling them as they are ruled during the rest of their days. The nasty whispers fade into blessed silence and the hole in his heart is miraculously filled as their two torn spirits join for a glorious moment of perfection. Then they break apart, and the whispers are back, but Yugi doesn't mind because he knows that he is not alone, and that makes all the difference.