A large dragon lives in a cave in the middle of a vibrant forest. He lives off instinct (hunting, hoarding etc.) with no sense of time. One day, creatures that look a bit like the deer he hunts invade his territory, and he scares them off. This event holds absolutely no meaning to him, except that he is angry about intruders.
Some time later, six intruders that look like the ones he scared off enter his cave (use descriptions of colour and shapes instead of names for the Mane 6). They linger a lot longer than the first, and appear to make noises at him before leaving. The next day, two new intruders enter his cave, taller than the others. He tries to scare them, but they do not relent. The Dark one's head glows, and suddenly the dragon is in pain.
Spike experiences his first flashback here. He and Twilight are having a minor argument, which Twilight wins by dismissing him and taking off. Spike thinks angry thoughts.
The large dragon shakes off whatever the dark one did, and attacks her, severely injuring her. The white one takes her away, though she lingers a moment after leaving the cave. The dragon goes to sleep, though he is wary of more intruders. He also experiences something akin to fear, and another feeling he cannot identify (anguish).
A long time after this (maybe a month), the dragon awakens to see a gem at the entrance to his cave. It is not one of his, but after some minor thought of where it comes from, he takes it. The same thing happens again for about a week. Then, on the next day, he awakens to see one of the intruders.
Instantly hostile, he prepares to attack, until the intruder levitates (he actually remembers that word, at this point) a gem. She places it on the ground before her, and slowly backs away, never taking her eyes off the dragon's. Suspiciously, the dragon takes the gem. The intruder lingers for a bit, then appears to vanish.
This happens every morning for a long while, with the intruder staying longer and longer each time before vanishing. At some point, he remembers the creature is called a pony. Eventually, the intruder appears with a sparkling red fire ruby, attached to some kind of necklace (this may or may not cause another flashback, author's choice). However, instead of placing the jewel on the ground, the pony places it around her neck.
The dragon is puzzled, but soon growls when the pony takes a step into his cave. The pony stops, then lowers herself to the ground. The dragon realises what it's trying to do: it's offering itself, as well as the ruby, as a part of it's hoard. It picks up the pony, who makes no effort to escape or struggle, and looks into it's eyes. Seeing no fear or deceit, he places it on his back, and takes it with him for the day.
The story has two parts at this point. The first part is made up entirely of flashbacks, detailing the events that led to Spike becoming feral (author's choice for this, though it should be Twilight who specifically causes it). These flashbacks occur when the dragon sleeps, or (when Spike remembers how to speak) as Twilight tells him stories about her/his old life. Near the end of the story, the flashbacks should instead be Twilight's, showing the Mane 6's reactions to finding Spike, her decision to be part of his hoard, and Rarity giving her the Fire Ruby in the hopes it would help.
The second part consists of Spike's life with Twilight (including feeding her), as well as him becoming less feral as time passes. Author's choice as to the progression for this, though a very important one is when Spike asks who the pony is, and she tells him she's Twilight Sparkle. Also, as he becomes more civilised, he should care less and less about the rest of his hoard, until eventually Twilight is the only possession he cares about. While this happens, he should shrink until he's roughly Twilight's size (maybe a head taller).
The ending should be where Spike finally realises that he actually is Spike, the dragon he's been dreaming of and that Twilight's been talking about. He asks Twilight why she/the Mane 6 did what they did. She should respond appropriately based on whatever it was (personal favourite is because she was scared of him being a dragon). She apologises, which Spike eventually accepts. Then he asks what's going to happen next.
Twilight says that that's up to him. He can give Ponyville/civilisation another chance, or they can stay here. An important thing here is that she insists she is still his property, and will be even if they do go back. Two reasons for this. Firstly, since Spike's new mental state was built entirely around Twilight, he will be very unwilling to lose her. Secondly, if Spike does decide to give Ponyville a chance, it sets up an interesting sequel where Spike tries to reconnect with the rest of the Mane 6 while keeping Twilight as a possession.