Shocking News

The tea cup shattered on the floor before anyone managed to grab it.

F: Discord, please, listen to me.

D: ...

Z: ...

F: I know this is a surprise to you. But this just felt like the right moment to tell someone...

Z: Oh, damn, sis. I did not expect this when you invited me over for tea!

Fluttershy sighed and looked back at Discord. She began to worry about him, he had frozen into a statue for almost five minutes now.
Zephyr cleared his throat and looked at the mess he just made.

Z: I'm so sorry, sis. But, you know, maybe you shouldn't burst out such shocking news when I'm holding something fragile. 

He smiled and Fluttershy snorted. 

Z: So, uhm. You're pregnant, huh? Wow. I mean. Family stuff. That's, uh, that's a big step.

F: Yes, I know. It happened, okay? I don't even regret it. It was my decision.

Z: You still gotta raise him yourself, you think you're up to that? Not that I think you aren't, because I don't.

F: I'm aware of that, Zephyr. And yes, I want to do this. It's my duty and I'll manage.

Fluttershy touched her belly with one hoof, it had grown a bit, but not that much yet. It was still early. She felt pride and fear inside her, and looked at Discord again.

F: DISCORD!

She suddenly yelled. Still nothing.

F: Don't make me fly up there, Discord. 

Finally, Discord closed his mouth and looked at her.

D: Sombra? King Sombra of all ponies? 

He still sounded shocked, but his voice was calm and low.

F: I wasn't myself for a while, you know that. I did many bad things, things I don't want to talk about. But afterwards, I don't know...

Her voice cracked for a second, but then she pulled herself together and straightened herself.

F: We had something. Yes, as weird as that may sound, we did. And he treated me well, even though he is responsible for a lot of suffering, which I don't deny or justify. 

There was a pause filled with silence.

F: It doesn't matter. All that matters is that I'm having a baby and I wanted to let someone know. I've known about it for a while and kept it a secret, because I was afraid of the reactions. But now I realize that was without any reason. 

Fluttershy gave Discord a hurt glare. Discord shivered and approached her.

D: I'm sorry, Fluttershy. I really am. It's just that...that the time you were with him was the worst time of my life. I was so afraid for you. I even fought this...

Discord grunted.

D: But it's true. He's gone. It doesn't matter now. I want you to know that you're not alone. I will always support you and the baby. You don't have to do this alone.

Fluttershy smiled and hugged Discord. 

F: Thank you, I knew I could count on you.

D: Always.

Zephyr tapped Fluttershy on the shoulder.

Z: Just to let you know, your secret is safe with me. I won't even let Mom and Dad know, if you want that. 

F: It's okay, Zephyr. Why shouldn't they? 

Z: Hm, that's nice. 

He grinned.

Z: Well, how long 'till the baby is due?

F: You'll know when it's here, I promise.

D: Uncle Discord - doesn't that sound wonderful? 

Fluttershy smiled.

F: It does!

Discord started to get thrilled about the idea of a sweet little filly or foal running around in Fluttershy's home. He could teach him or her so many things!
The only thing that kept his joy from bursting was the little thought that crawled in the back of his head:

What influence will Sombra's genetics have on this child?

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Wow look at that! The old headcanon finally continues! 
This occurs after:
this  , this   and this  .

Basically, King Sombra wanted to start another war. He was filled with rage and the desire for vengeance, but I'll be more clear about his motives in other pictures. He kidnapped Fluttershy and kept her as a prisoner at first. With his little recruited army of hypnotized ponies (black magic) he managed to fight Celestia's armies quite well. Later, Sombra realized hypnotizing Fluttershy would only make her more useful. It had a strong effect on her, and she turned into a cold blooded War Queen, not afraid of slaying her enemies and making no prisoners. But the real Fluttershy was still inside and fought the black magic. 

In the course of events Sombra started to catch feelings for Fluttershy and removed the spell from her. She then suffers quite a lot with guilt and the consequences of her actions as a War Queen. Sombra then starts to doubt his plans and his rage begins to disappear. Slowly the two of them get closer, even though Fluttershy is extremely angry at the beginning. But Sombra accepts this, frees all his soldiers and stops the war.

At this point, Sombra has grown on Fluttershy, and she decides to stay. They spend quite some time together, hidden from Celestia's search troops and the worried Mane Six.

Finally, though, Sombra sees that Fluttershy isn't ultimately happy like this. So he tells her to go and that he can't ever return.

Fluttershy then is found in a forest by the search troops and being taken back to Ponyville.

Discord is in full rage mode, of course. He manages to find Sombra after a long search and fights him, without letting Fluttershy know. But before Discord could beat him, he disappears again. Just like that. Discord gives up and returns to Fluttershy.

And then...about 2-3 months later, this scene takes place.

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I hope it's not too confusing. Please don't ask for too many details, the story is not finished yet. But you can ask questions if you are interested.

Fluttershy and her foal: