Amore

Setting: A Canterlot Wedding (S2E25-26), and the days following.

When Chrysalis brainwashes and steals Shining Armor's love, he spend the time brainwashed dreaming in a loveless world. This world is Earth, and Shining Armor believes he's a 20-year-old human living a rough, lower-class lifestyle from paycheck to paycheck, with no family, friends or lover to help him. This is a traumatic, magical process, and causes most of Shining Armor's memories as a pony (memories filled with love) to disappear, essentially leaving behind a different person. Fragments of what he remembers take the form of the television series and IDW's comic series (in the story, this assumes Shining Armor reads the letters Twilight sends to Celestia, as a way of keeping in touch with her). Beyond that, he has no knowledge of Equestria or his life as Shining Armor.

As Shining Armor fights back against the spell, this comes in the form of bizarre dreams for the "human". These dreams appear to replay scenes from the episode A Canterlot Wedding, with the "human" taking the role of Shining Armor. In reality, these are brief moments of lucidity for the real Shining Armor, as Chrysalis's magic loses it's effect; however, the "human" is unable to realize it as anything more than a dream.

His subconscious permeates the dream world of Earth, slowly transforming him from a human into his true form, a pony, specifically Shining Armor. The human has no explanation for it, scientifically. The only other coincidental even taking place was receiving an unmarked mystery package containing a Shining Armor plush. (This is a callback to the original premise for the Pony Transformation general on /mlp/, as well as explained to be Luna intervening into the dream to remind the "human" what his true form looked like.)

When Cadance breaks the spell on Shining Armor, and the duo use their love magic to banish the changelings from Equestria, Shining Armor passes out from exhaustion and sends him into his final dream as a human. By this point, the "human" was so mentally invested in the dream world, that the absence of Chrysalis's input causes the dream world to break down, and marks the complete transformation from a human to a pony. The stress and magical trauma inflicted on him threatens to send him into a coma he won't be able to recover from, represented by the dream coming to a climatic ending point, and the implied death/capture of the "pony in Earth." Luna intervenes, and "rescues" Shining Armor from the dream world.

This puts the now loveless version of Shining Armor into the body of Shining Armor, as the actual wedding takes places. From there, Twilight, Cadance, and Luna start to piece together what the effects Chrysalis's magic on Shining Armor actually entail, and the reader is intended to discover this alongside the "new" Shining Armor. Eventually, the big reveal happens: the "human" never actually existed, and that his personality is that of Shining Armor without his love and memories. He was, technically, Shining Armor all along.

He then turns to Twilight to ask if she can find a spell to restore his memories. She says that she's willing to learn, but that Shining Armor must come to understand the gravity of what he is asking. Essentially, if Shining Armor's memories are restored, the "hole" in his memories will be filled, and the personality that formed because of that "hole" would cease to exist. Twilight reasoned it as him asking her to kill this new personality, in order to bring back the original Shining Armor, and that she would only do so if the "human" personality understood that.

Regardless, it takes a bit of time, anywhere from a month to three months. During that time, Shining Armor dates Princess Cadance, and falls in love with her all over again. She remarks that it's unfolding exactly how it did in the past, and that this "loveless human" personality reminds her of Shining Armor when they first met. He also goes onto hijinks in Ponyville, living out the dreams any My Little Pony fan would have if they were given the chance to live in Equestria.

Eventually, Twilight finishes the spell, and informs Shining Armor, who is disappointed. He now understands why Twilight told him he had to understand the meaning behind the choice: he has been enjoying the dream life in Equestria, and he now wonders if he can "end his life" to return Shining Armor. He takes the day, alone, to think about it. In his dreams, he comes into contact with the real Shining Armor personality (or, at least, what he thinks is--the truth is meant to be vague). After a deep explanation, Shining Armor jokes, says that Twilight is always prone to overreacting, reminding the "human" of the events that took place in Lesson Zero, all because Twilight was afraid of being tardy with a Friendship Report. He reminds the human that he won't be losing the memory of the events that already took place, and that no matter how his way of thinking changed, he will always have the memory of what took place the past few weeks, and that is proof enough that he had existed.

The next day, Shining Armor asks Twilight to perform the spell. The story ends as Twilight's magic engulfs Shining Armor, leaving it on an unsure note, all Inception-like.