|"Oh Rainbow..." Twilight sniffled, shaking her head. "Silly...silly Rainbow..." She reopened her moist eyes with a bittersweet smile. "I'm not sad."
"Well... uh..." Rainbow cleared her throat. "Don't be soggy then."
|- Ynanhluutr, "Second Chances are Miraculous Things Indeed"|
Twilight Sparkle is dead, and has been since chapter one of Austraeoh.
She and the rest of the Elements of Harmony tried and failed to fight Discord, and were all atomized when they failed. However, because of the process of Harmonic Acclimation which had already taken place, her soul was bound to the incorporeal Element of Magic, which took up residence inside the nearest physical vessel, which was Rainbow's Element of Loyalty. Her appearance implies that the rest of the Mane 6 have a chance to be revived.
She seems to be directly related to both the Yaerfaerda (Symbol) and the Lavender Light, as, obviously, they are both her signature purple. Even more tellingly, after her appearance as an incorporeal form on the island at the beginning of Ynanhluutr, the Yaerfaerda beacon turns pure white, perhaps denoting Rarity will be the next illusion/ghost to appear.
She is completely invisible and incorporeal, as evidenced by her trying to interact with objects and produce only a lavender light. This has proven helpful in scouting things out through solid walls or underwater. There are subtle hints that she may be able to make herself more "substantial" either through concentration or habit, as when she's "trotting" on the ground, feeling the wind, smelling things, etc.
She is bound to the Element of Loyalty pendant, which keeps her confined to a radius of about 6 meters from Rainbow Dash at all times. Since joining up with Rarity, this confining distance has been expanded to approximately 30 meters. When she feels tired she can "sleep" in a mysterious hammerspace that seems to be inside the pendant itself.