A/N: Maybe Shoko's soul is supposed to be completely gone, replaced by Cossette's... but that's not the way I see it. This is my take on how Cossette was reborn into Shoko.
Shoko's soul was engaged in the struggling ascent back to consciousness when she became aware of another soul in her body. It was sweet, delicate—but strong—a soul like a whispered secret.
Please, said the little soul. Will you—
Will I what? Shoko's soul prompted. She was confused and a bit resentful of this strange newcomer, but she was determined to be at least civil to it—to her. For it was undoubtedly a feminine soul.
I— She paused. You—you love Eiri, don't you?
Shoko's soul was taken aback. Well, I... yes. I do.
I love him, too, the little soul admitted.
Wait—are you—you're the girl Eiri fell in love with!
The little soul made a small movement like a nod of assent.
Then why are you here? Shoko's soul could not entirely conceal her resentment, which had escalated when she learned who the little soul was.
Because I'm dead, the little soul responded simply. I've been dead the whole time he knew me, but I'm—I'm free now. I'm at peace. And...
It's time for me to be reborn now, said the little soul. And I... can I... Will you let me stay with you?
With me? Shoko's soul did not even try to hide her disbelief.
Yes. Because he loves you now—or he will soon—and I... don't want to lose him. Please, let me stay here with you.
Shoko's soul brightened as if with a blush. Did Eiri really—would he—? From the dream, or vision, or whatever it was that she had seen, she had suspected it. But for someone else to say it, someone whom Eiri loved...
The little soul waited in silence.
Shoko's soul struggled with a myriad of conflicting feelings. She was happy at what the little soul had told her, yes, but—she didn't want to share Eiri, especially not with someone whom he had already chosen over her! She had no obligation to this delicate, whisper-soft little soul who so sincerely asked for what she wanted more than anything else... who wanted Eiri.
For a split second the thought occurred to Shoko's soul that Eiri might love her more if she carried with her the soul of his beloved, but she dismissed it quickly. The thought that seized on her a moment later was this: that Eiri really did love this tender little soul. And if Shoko really loved Eiri, shouldn't she love the little girl's soul because Eiri did?
Yes, she said at last. I would be happy to have you stay. It took an effort to say it, but she knew that it was right.
The little soul seemed to glow suddenly, with an internal light. Thank you, she said softly, in a tone that pulsed with the deep love of ages.
The little soul—whom Shoko's soul later learned was called Cossette—was quiet and unassuming. For a while, Shoko's soul deliberately spoke with her, and made special efforts to be kind to her. In time, they became friends.
But as Eiri finally, finally, began to fall in love with Shoko, her secret soul grew more and more caught up in him. At last she began to forget that she had ever accepted another soul into her body. Shoko grew softer, more tender—not much, but a little. Just enough for Eiri, every once in a while, to wonder.
More time passed, and Shoko did not remember the soul of little Cossette until the day that Eiri asked her to marry him. And when her soul sought for the whisper-soft little soul of the other girl, she found herself alone.