Amongst all the sounds for the PC version of Shadow of Memories can be found voice files for an ending not used in the final product. The fact that the dialogue was actually recorded for it suggests the ending was removed fairly late in production. A short summary of the ending is as follows.

It begins with Homunculus revealing the truth about Eike's connection to Dana, and in turn, his non-connection to Margarete. He is amused at the quirks of fate making time always realign itself to the correct path when drastic changes are made. Eike then travels back to the Lebensbaum of the 1500s to fulfill Margarete's wish to see the future. Along the way, the Digipad begins to malfunction, so upon arriving in the future he questions Homunculus about it. Incensed that Eike has the audacity to suggest his creation could be so fragile, Homunculus goes to examine it, only to have to break before he manages to look at it. A lethal fragment of the device pierces his temple, causing his lifeblood to spill onto the markplatz floor. Homunculus dies and Eike muses on the quirks of fate with Margarete, just as Homunculus did before him.

The similarities in the climax of the scene with that of Ending A (Homunculus' death caused by a broken fragment of the Digipad piercing his head) leads us to believe that the developers may have planned at one point for there to be alternate versions of Ending A. Perhaps there would have been Endings A1 and A2, as there is with Ending B, with B1 and B2. This us further supported by the fact that Margarete is worried about being Eike's ancestress. This shows that this ending would have belonged to the group of endings that become available after choosing to tell her you think she is your ancestress.

A full transcript of the scene can be read below. Some of the words are difficult to make out, so corrections would be welcome.

*The scene opens in the Marktplatz, present day.*
Homunculus: Oh? Unfinished business? Hmm... Would you like to go fetch that confounding(?) Margarete? You've probably figured this out by now, but Dana's gone home to the past. Yes... That blonde girl? She's related to you, you know.

Eike: You really expect me to believe anything you say at this point?

Homunculus: Mm-hmm. Really? Well. You can believe whatever you like? As for that Dana girl, things may have been gotten a little 'mussed up' at birth. But her life turned out the same anyway. I didn't even have to fix anything. It really is remarkable how destiny skirts back to the way it was. This one even surprises me! So, will Margarete be joining you in this age? *Pause.* Well? I won't be too gross(?) about it, then. Just one more time. Wherever you're going. And that's it, Eike...

*Scene change to the past. The sound of Eike's approaching footsteps can be heard.*
Margarete: Eike? Is that you, Eike?

Eike: Yeah.

Margarete: Look at this! It's just me now! Everyone else is gone. *Pause.* Did you know about this? That this would happen?

Eike: No, I didn't!

Margarete: Won't you take me to your time? Or is it still a 'no' because I'm your ancestress?

Eike: I'm sorry. I made a mistake about that.

Margarete: What? Really?

Eike: It was one of Homunculus'... Ah well, I guess it doesn't matter. So... I thought if you like, I could get you to come with me. I know you'd like to see that age. How about it?

Margarete: All right. I'm ready. Let's go.

*The Digipad makes a strange noise.*

Margarete: Ahh!

Eike: You okay?

*Scene change to the present with Homunculus again.*

Homunculus: Welcome back, Eike. Time to give that thing up.

Eike: Yeah, about this thing. It did something weird just now. Maybe it's broken.

Homunculus: As if anything I make breaks down so easily. Here, let me have a look.

*Eike goes to pass the Digipad to Homunculus, but ends up dropping it. It clatters to the ground and a sharp shard breaks off from it, piercing Homunculus in the head.*

Homunculus: Oh no! *Screams as he dies.*

Margarete: What happened?

Eike: I think it was... destiny. Maybe fate decided his life would end this day.

The ending can be heard in four parts from the links below.

Secret Ending Part 1
Secret Ending Part 2
Secret Ending Part 3
Secret Ending Part 4