Weeks after the dramatic battle with the Deer... And Ponyville was back to normal... Shepherd was walking around, taking a day off. He headed up to Filthy Rich's store to do some shopping... When he saw them. His eyes widened as the Cutie Mark Crusaders happily bouncing out of the store.

Shepherd: "Huh. Hey girls!"

Applebloom: "Oh! Howdy Shepherd! Look what we got!"

Sweetie Belle: "They're on sale today!"

Scootloo: "And look totally awesome!"

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Just an older snippet I will probably repurpose for Short Hand eventually.

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Spike is helping Rarity with her work. Ever since Twilight ascended and Shepherd's helped coach him through controlling his greed, he's become taller and bigger. And in many eyes, far more handsome.

Spike: "Here, this is the needle you want."

Rarity: "Oh, thank you dear... Hm?" She looked over at him more closely, and saw that he was distracted. "Spike, I need the red thread next."

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At last, the day of the Eeeevil Imperial Wedding has arrived! Shepherd is in big, bulky, "impressive" looking evil wedding armor. He is standing at the Eeeevil Altar erected in the Palace Courtyard, Discord waiting as the 'minister' and Cadence is sitting nearby as Mare of Honor. Chewie is "Best Stallion", and standing with a large bowtie as he growls, while Spike is the ringbearer, again.

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A number of events in the series will be butterflied away thanks to Shepherd being around. Among other things...

The Storm King's mighty airship approaches Canterlot...

Storm King: "Yes... Soon, all of Equestria will fall before me and be laid waste-"

And the much larger USS Enterprise CV-6, flying the colors of the Royal Equestrian Navy, loomed into view.

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Shepherd: I've known her the longest, and she's been fairly obvious... Okay blindingly obvious with her affections. So let's just man up and ask her. Clearly, she's too shy to just say it.

He knocks on Fluttershy's door

Fluttershy: Opens it "Oh... H-Hello Shepherd. It's so nice to see you, how are you?"

Shepherd: "I'm good. So. You want to go on a date with me this Venuday?"

Fluttershy: "..."

Shepherd: "... Fluttershy?"

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Shepherd tries to Help Twilight Sparkle

After Twilight Sparkle ascended to Alicorn, and became a Princess, her relationship with Shepherd didn't change too much. He was already a knight assigned as the guard for the Elements of Harmony after all. He did have a lot more duties involving her though. Unfortunately they usually involved paperwork.

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Shepherd took the revelation that Doctor Whooves and Ditzy had a time travelling, dimension-hopping muffin-shaped TARDIS quite well.

Shepherd: "HOLY FUCKING SHIT WHAT THE PUS SPEWING FUCK-!"

But after he was able to compose himself, breathing into a paper bag in the main control room of the Muffin...

Doctor: "Now now, everything is all right!"

Shepherd: "So... You think you can get me home?"

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Tea Time at Twilight's Palace...

Fluttershy: "You know Twilight, you've been spending a lot of time on reforming villains."

Twilight: "Well, what can I say? You inspired me! With the work you did with Discord! Now he's... Completely... Devoted to you..."

Fluttershy: deadpan "Twilight. No."

Twilight: "I-I didn't do-I'm not doing anything!"

Fluttershy: "I know you! You're going to concoct some kind of... Crazy scheme!"

Twilight: "Am not!"

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Twilight saw her other friends. All of them twisted and changed by the harsh war. It was heartbreaking to see them all like this. Fighting for their lives to save Equestria. And there was Shepherd...

He walked to a shack, and Twilight followed him. He looked over his shoulder at her.

Shepherd: "Something I can help you with?"

Twilight: "I... You're human."

Shepherd: "And you're an alicorn."

Twilight: "What?! How did you-?!"

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Shepherd is studying in the library. This isn't surprising. But what is surprising to Twilight is who he's studying with-Pinkie Pie!

Shepherd: "So, there is a similar mass extinction cycle in this planet's natural history?"

Pinkie: "Looks like! Maud's been doing research into it! And it's nice to meet another person who can understand what she's talking about!"

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Andrew somewhat reluctantly stepped into the library, having received a letter from Twilight asking for his presence.

The fact it was a letter, and she hadn’t just come over to talk to him, or asked somepony to speak to him next time they saw him, was slightly ominous. Either something official, or ‘hijinks’ were looming on the horizon.

Either way, he felt his trepidation was justified.

However, no one seemed present.

“Twilight? Spike? It’s Andrew. I came? About your letter?”

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One night, while Shepherd is reading at home... He hears some bells ringing, and then his walls turn purple. He sighs, and closes his eyes tightly.

Discord: "Guess who?"

Shepherd: "Not in the mood."

Discord: "Aw, why must you be so hurtful, Shepherd? After all, I am reformed! Fluttershy said so herself!"

Shepherd: "Yeah, and I'm still checking her for mind control magic or body swapping or literally anything else you may have done to her."

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Shepherd: "Twiliiiiight! What the hell-Where did all these bits come from?!"

He gestures to the pile of gold bits on the kitchen table.

Twilight: "Ummmm..." taps her hooves together "I asked for donations from all the research participants... I set fifty bits as the minimum donation and well..."

Shepherd: "... If I didn't know any better, I would swear you were pimping me out."

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Consider this a rough draft...
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So, our lovely mares and Shepherd had to go and try and get a dragon to leave the area around Ponyville. His 'nap' might last for a century, and the smoke he emitted would make it unlivable. However... Fluttershy was terrified of the prospect of confronting a dragon.

Frankly, so was Shepherd.

Fluttershy: "Um... I mean... Maybe we could just... Just move the town?"

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Nightmare Night, and Shepherd is chilling out and enjoying the festivities.

Dash: "Hey Shepherd! Eh? Who are you dressed as?"

Shepherd: "I'm the Doctor!"

Dash: "Doctor Who?"

Shepherd: "Actually the Eleventh but..." At Dash's blank look, he sighs "Nevermind."

Dash: "Anyway, you look like... A dork! Especially with that bow tie!"

Shepherd: "Bow ties are cool, thank you. I was just going to go see Fluttershy."

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Shepherd has finished his morning training with Chewie. He walks up to his house, where the Elements of Harmony are relaxing in his backyard.

Shepherd: sigh "Why do you always hang out in my backyard?"

Pinkie: "You don't change your locks often enough!"

Dash: "Wow Pinkie. Just going out with that?"

Pinkie: "It's a joke, silly! Shepherd knows this!"

Applejack: rolls her eyes "We also brought food and booze."

Shepherd: "You're immediately forgiven."

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After the Changeling Invasion and the wedding, Shepherd was trying to relax in the armor and weapons from the Ancient Human Archives he'd pilfered for the fight in a small, unoccupied room in the palace. After some time, Princess Celestia entered, sat down next to him, and began eating cakes too.

Shepherd: "... You okay?"

Celestia: "... Shepherd. Do you think I'm weak?"

Shepherd: "Huh?"

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At Canterlot Palace, Shepherd is pacing back and forth and trying not to trip over his own cape.

Blueblood: "The entire Crystal Empire fleet is heading this way, Your Dreadfulness."

Shepherd: *groans* "Oh good! More pressure! I don't suppose we could just tell Shining this is all a wacky sitcom plot?"

Raven: "Alas my Dark Lord, he is unlikely to believe you."

Applejack: "To be fair, he does kinda hate yer guts anyway."

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Among the other artifacts of humanity in the Everfree Dump was, of all things, the fully armed and operational turret of an Iowa-class battleship, all three 16 inch guns intact.

And Pinkie Pie got to it first.

Pony: "Oh thank Celestia you're here Miss Pie! The children are getting restless! They tried to eat Shepherd!"

Shepherd: "Back! Back!"

Pinkie: "Time for the big guns!"

Pinkie Pie pulls out a field radio.

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