After Stygian disavows his persona as The Pony of Shadows, he begins to observe the resurrected Pillars of Equestria as they adapt to a modern society. It proves a tad difficult for the lithe unicorn. Of top of attempting to adjust to all of the changes the world had gone through, Stygian continued to fight with his regret - of what he put his beloved friends through in the pursuit of power and respect. Its almost like a different kind of darkness spreading through his soul. He pours his heart out into his first book in eons, and it becomes a best-seller.
 
However, this doesn’t improve Stygian’s dark mood. Out of desperation, Stygian writes a long, sorrowful letter reaching out to Princess Twilight Sparkle. He remembers Starlight describing how the princess saved her from a darker fate, and expresses his eternal gratitude for reaching out and pulling him away from the anger and hated. Touched by his kind words, Twilight invites the unicorn to stay in Ponyville for awhile, feeling it better to gradually re-introduce him to the world, and Ponyville being the perfect peaceful place to start Stygian is hesitant at first, but eventually arrives on the Ponyville Express, telling the princess he is ready to try and live his life once more.
 
Twilight immediately takes him under her wing, eager to have another student. However, as she begins to observe Stygian interact with the ponies around town, she sees the pony he once was - kind, compassionate (and appreciates his quiet time - just like she does!) He is in absolute heaven when Twilight shows her his extensive library.
 
From there, the two begin to bond over their various fields of study and spend long, late evenings sharing notes and comparing reports. Stygian is enamored with Twilight’s research and she uses it to help him learn about the thousand years he was trapped in Limbo. Stygian, with her help, begins to slowly become more at ease with his new life. New technology, discoveries and advances in science fascinates Stygian, and Twilight relishes in teaching him all she knows. One night, while taking an evening stroll through Ponyville Park, the two bear witness to Luna raising the moon and stars. Stygian reminisces about the last night he sat and watched the beautiful night sky. They sit together and observe the night as he thanks her with sincerity. He thanks her for not only re-introducing him to the world and all the beautiful things it has to offer, but also for being a simply wonderful friend and having faith in him. Twilight is touched by his words, and when he catches him staring at her while talking about how beautiful the sky is, she feels a weird, warm tingling in her tummy.
 
For the next few days, Twilight can’t help but spend a little more time with Stygian, prolonging their lessons and much as she can. During such, she researches all of her student, strong symptoms. Is she ill? The victim of a hex? When her research yields no surefire results, Twilight actually finds herself confiding in Princess Cadence while on a diplomacy trip. She reluctantly makes her inquiry, having a building suspicion her weird feelings have something to do with the gray unicorn.
 
Cadence quickly confirms Twilight’s first real, really real crush.
 
A tad freaked out, as the world of romance is a bit of a foreign concept to the alicorn. She is rather flummoxed and her distance makes Stygian worry that he’s done something to upset his new friend, and may be delving back into the darkness again. The tension between the two finally comes to a boil when a vicious Stryx escapes from Tartarus and attacks Ponyville. Twilight fights it back after she and Stygian are ambushed while on a walk. He desperately searches for a spell to defeat the horrid creature. He successfully finds text on an ancient mcguffin talisman that may be able to defeat the monster. After going on a quick journey and retrieving it, another battle occurs and Stygian is nearly corrupted and killed by the Stryx. He manages to defeat it just in time.
 
Twilight angrily asks him why he did such a thing, he quietly reveals his gratitude. He couldn’t stand to see such a wonderful pony get hurt. Twilight reciprocates his feelings in a big gooey scene of lovey-dovey goodness.
 
The two currently reside together in Twilight’s castle, Duke Stygian now researching new types of shells that have evolved over the last thousand years for his next book. He’s made some fairly fascinating discoveries so far!
 
 
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otp :3