This takes place after Atem returns in Season 5, in episode 203. This is Mana's reflections after their meeting and her confusion. I'm sorry if some of it doesn't make sense, but it's just something that came to me and I had to write it.
Disclaimer: I don't own Yu-Gi-Oh or any of its characters.

My friend, how I miss you desperately.
Why did you have to leave?
Why couldn't you take me with you?
Are you going to return?
Are you going to come back for me?

So many questions, all ones that no one can give me the answers for.

I wanted to tell you,
but I lost my nerve.
So now I'll say it, and hope you hear it, wherever you may be:
I love you. I love you with every ounce of my being.
I would give anything to be with you.
I wished I'd said something. But . . .
when I saw you after the ceremony,
You seemed different. More distant.
It was like your memories had disappeared or something.
But, you wouldn't forget about me, right?
Like I said before: "you and I are practically family!"

I love you. I was planning on telling you that after the ceremony today, except . . .
well, for one thing, Mahad was with you, and for another . . .
it wasn't you.

You didn't know me. You tried to hide it, but it's like all your memories have vanished.
I'm desperately worried about you. Has there been an accident?
Or . . . are you acting that way because you're Pharaoh now, and I'm just a lowly apprentice?

I wanted to talk to you, but I couldn't bring myself to, not after our second meeting.
I mean, you asked me to tell you about us! What was that about?

I'm almost convinced that someone or something has taken over your body, or worse, they're impersonating you!
If it's the latter, then where are you? What's happened to you?

I miss you. And I want to help you. The one thing that worries me the most is that you've simply decided to ignore me.

I love you. And I dearly hope that the feeling is mutual. Could you tell? From all the time we spent together? Could you?

Please don't forget about me, wherever you are.

Again, I'm sorry if it's a little confusing. I hope that it was okay and that you liked it. If you could, please review! I'd love to see what you thought about it. Thank you everyone!!