This is what I believe that happened in the small lapse that we didn´t see Hei in the last chapter of season 2. Because he was in that weird room in one scene and in the other is in center of the Gate. I hope you guys like it. (And please forgive my spelling or my mistakes, is the first fic I do in English. Please have mercy)
It is not too late.
"She stopped the awakening herself?"
"That´s right. On the day we retrieved Izanami, we had originally planned to kill her right away. However, right before we were going to, her reactions as Izanami had stopped. Knowing what her powers are when awakened, we hurried to seal her away here. Until you destroyed that. We had hoped that she would choose to fall asleep again on her own. However, a second miracle didn´t occur….I´m not blaming you, there was nothing humankind could do from the very beginning, ever since the Gates appeared in our world."
Hei heard all of that without change his indifferent face, but…those words….they hurt him.
"Yin" he whispered "Let´s end it all"
"What are you going to do?" asked Kobayashi.
Hei stood up from the floor, feeling miserable inside. He had never wanted any of this; he had never wanted to become Yin a monster, a murder. He just…he just wanted to be with her in a peaceful life. But now that was impossible, and it was his fault.
He gave a last look to Yin´s body and finally answered.
"I´m going to kill Izanami" Why he sounded so calm outside when he was suffering inside? Hei knew the answer: he was a contractor, he wasn´t suppose to show emotions, Hell he wasn´t even supposed to HAVE emotions.
"I´ll help you to get to the center of the Gate, that´s all I can do" proposed the man. Hei nodded at once.
After that both men got out the room.
They got into a car and drive to the tunnel that was under the Gate. Hei remembered the last time that he had been there, almost two years ago. He remembered Amber, and how she gave him the chance to see his sister once again, and solve the mystery of what was he. After that moment he lost his reason to keep fighting…and then…he heard Yin´s voice, begging him to come back. "Don´t leave me all alone! She had cried.
"What is it?" asked Kobayashi, getting Hei out of his thoughts.
He had made the question because Hei´s face was painful, and he had stopped walking.
"Nothing" he answered.
As he said those words, a bomb exploded near to them. Kobayashi took a gun a started to shoot. In was the CIA.
"Run!" screamed Kobayashi "A ghost spirit will help you to get to the center of the Gate! You still have a chance!"
Hei hesitated for a second, but then he run away. His words echoed in his mind as he ran.
You should believe in me too…I won´t leave you alone.
He said those words when they were running of the Syndicate. In those days he really meant it. He wanted Yin to trust him.
You are lying.
Did she know that he would break his promise? He didn´t know the answer and that fact was killing him inside.
Finally he saw a ghost spirit and he followed it.
I love you, Hei. And I don´t want to forget it…but…we can´t be together anymore.
Yin had said that the day she separate from him, crying.
If we ever meet again, then….
She hadn´t finished the sentence, but he knew what she wanted to say ´If we ever meet again, then kill me´
After a few minutes following the ghost, Hei finally got to center of the Gate, but Izanami wasn´t there. In that moment the ghost went to a meadow. He followed it.
In the meadow Hei saw a lot of corpses, corpses of contractors, and then he saw a thirteen years old girl, with a big gun and red hair. She was Suou.
Near where she was Hei saw a little pale woman. Izanami.
Suou was crying, her face full of pain. Hei wondered if Izanami was torturing her.
Finally Suou reacted and screamed "DON´T ERASE THEME!"
Hei sat near to her and stopped the shot. He knew that Suou was dying and the only thing he could do was hugging her.
"Who are you?" asked the girl.
Hei took the gun "You are not going to need this where you´re going" said Hei, somehow he knew that she would be in a better place now.
"Where are going next? We can continue our journey? ...we… will always be together, won´t we?" her voice sounded so weak, so fragil. He didn´t contradict her.
"Yeah, that´s right" he reassure her.
"Lies" this looked so similar to the conversation that Hei and Yin had once.
"I´m not lying, I will always be by your side" he brushed her cheek as he said that.
"…Hei" that was the last thing she said. He carried her and laid her beside July.
Then, he felt a hand on his shoulder "Hei" He knew that voice, he would recognize it anywhere. He turned around and looked Yin´s face. She looked a little worried.
"Yin" said Hei, she smiled.
"It´s not too late. Kill me"
Hei really expected her to say that. He smiled, resigned, as he stood up.
"I love you" she said when Hei´s hand end in her shoulder. She looked just as he used to be before all of this happened.
A few moments before a white intense light covered the Gate, Hei answered.
"I love you too" and then everything became white.
The end.