Then I’ll ramble a bit to get it off my chest, and if no one else takes an interest, I’ll let it drop.
Warning: This is where open spoilers start. Massive, complete end-of-game spoilers. I’m not putting the wall of text in a box. Read on at your own risk.
So: the tricos are enslaved, trained to kidnap people–maybe children specifically–from villages surrounding the valley. They bring them back in their crops and dump them into a chute on top of the central tower and get rewarded with barrels of Trico Snax. The whole process seems to be controlled by the sphere in the tower that the boy calls “The Master of the Valley”. The Master is affected by the mirror, which seems to push it into a dormant/restart state briefly. In the midst of a heartwrenching sequence, the boy uses the mirror and Trico’s tail to destroy the Master. The physical and magical aftermath of this event leaves the boy unconscious. Most of the other tricos, disoriented by the sudden cessation of control, fall off the tower, presumably to their deaths.
Trico, terribly injured, finds the unconscious boy inside the crumbling tower. He takes the boy and makes a desperate flight to the valley’s wall and eventually back to the village from which he had originally taken the boy while under the Master’s control. He crashes in the village and coughs up the boy, who is picked up by a man (possibly his father). With the villagers preparing to kill Trico with spears, the boy wakes and musters just enough strength to order Trico up and away, so that neither he nor the villagers would be further harmed.
Many years later, a child finds the half-buried mirror, which apparently fell unnoticed somewhere in or near the village. The boy–now apparently an elder–tells the children the story of his journey (hence the narrator). He holds up the mirror, and its light awakens again; the camera follows its beam up and soars all the way back to the valley, to the room where the boy first awakened. In the darkness, gleaming eyes open–perhaps Trico’s–and are then joined by another set. Soft sounds become audible that suggest possible baby tricos. (No babies are shown, however. Possibly because the world could not bear such adorability.)
So, yay, that’s the game. Story told. It’s all about the relationship between a beast and his boy, and how they win their freedom. That said…what the hell was going on? What was the Master? Who built the city? What happened to them? What was in the Trico Snax barrels? What were the suits of armor? Why were people being kidnapped?
So, here’s my notion about the backstory. I think it covers most stuff adequately. Feel free to knock holes in it, if you’re interested.
Long ago, an explorer found a way into the valley. There he discovered something extraordinary: a spring with healing powers, guarded by a colony of great flying beasts. He returned home with his tale, and an expedition formed to claim the spring.
In the beginning, the colonists befriended the tricos and shared the waters, but in time, they discovered that the source of the spring’s powers lay in a substance leeched into it from below. In its concentrated form, it held far greater power, and they began to mine for it and learn its uses: from extending life and creating ever-burning flames, to enchanting metal devices, supporting fantastic constructions, and controlling the tricos. Jealous of their new-won power, the colonists sealed the valley, so that the only way in or out was through the air.
They built a vast and towering city, but in the end, the price came due. Perhaps it was due to side effects of the mysterious elixir, or maybe it just began to run out. Maybe it was simply their isolation. Regardless of the cause, their numbers began to dwindle. To maintain control of the valley, they created the Master, an AI-like magical construct, and gave it Eyes all over the city. They began using the tricos to kidnap villagers from surrounding lands to use in the creation of construct warriors and servitors. As they continued to dwindle, they gave over more and more tasks to the Master–control of the servitors and tricos, the mines, everything. When the last human died, the servitors entombed them at the base of the Master’s tower, their sarcophagus marked with the symbol and focus of their power–the Mirror.
The Master scarcely noticed. It continued its tasks: mining, kidnapping, creating servitors. An endless, pointless cycle of slavery…until a wounded beast and a young boy broke the cycle, freeing the valley to return to eventually return to its natural state: a place where magical waters run and wondrous beasts fly free.
Bonus bit: I’d like to think that the spring, the pool in the sarcophagus chamber where the boy finds the mirror, and the pool in the temple in Shadow of the Colossus are one and the same.