1,500 years from modern times, the place now known as the Ruins of Alph was built in Johto, and the earliest system of writing was developed. Nobody knows exactly who built the Ruins of Alph, but research indicates that they were most likely an ancient civilization that wished to co-exist with the enigmatic Unown that bear great resemblance to letters from our modern Latin alphabet. Not only did the ancient people impart messages in the ruins' walls describing the Unown, but a statue of a Pokemon was also erected for reasons unknown.
At some point later, outsiders began to gather near the ruins. The Unown were timid creatures, rejecting contact with anyone but the ancient clan who had protected them. To make sure of the Unown's well being, the Ruins of Alph's inhabitants decided to leave Johto, but not without devising complicated puzzles so that the Unown could be summoned again. As for the clan, they headed for a mountain in the far north where they met another group of people who hailed from Spear Pillar. Together, the two groups constructed a temple to honor the Pokemon, Arceus, which incorporated elements from the Ruins of Alph and Spear Pillar; this collaboration probably has something to do with the relationship between Arceus and the Unown. The temple, too, has been since left in ruin, and its lowest floor is known today as the Sinjoh Ruins. However, the ritual of honoring legendary Pokemon goes all the way back to ancient Johto, specifically Ecruteak City.
About 700 years before modern times, the people of Ecruteak built two large towers with the hopes of fostering friendship and hope between Pokémon and humans, the Brass Tower in the west, which was said to awaken Pokemon, and the Bell Tower in the east, which was said to put Pokemon to rest. Both towers became the roost of two powerful flying Pokemon, Lugia and Ho-Oh, respectively. Although it is unknown what made the citizens of Johto revere Lugia and Ho-Oh, a seperate tale indicates that Lugia had had a previous encounter with the people of Johto when it stopped a war on the Whirl Islands, which were a single island at the time.
The towers stood for a good 550 years, when a lightning bolt struck the Brass Tower. It was engulfed in flames, and the fire lasted for three days. Finally, a sudden downpour came and put out the blaze, but it had already burnt to the ground. Three nameless Pokemon perished in the fire, but Ho-Oh descended from the sky, and ressurected them. The revived Pokemon were meant to embody three powers: the lightning that struck the tower, the fire that burnt the tower, and the rain the put out the fire, and thus, the legendary beasts, Raikou, Entei and Suicune were born. When the three appeared, the struck terror into those who saw their rise. Then the Pokemon, knowing their own power, fled, running like the wind, off into Johto's grasslands. Both Ho-Oh and Lugia flew away at the sight of the growing distance between people and Pokemon. While they never returned to Ecruteak, they yearned for a person to touch the hearts and souls of Pokemon once more.
Around 500 years from modern day, the Cianwood City Pharmacy, the world's oldest pharmacy was built. About 400 years ago, Azalea Town was struck by a long-term drought wave. After once again bringing the rain back by yawning, the Pokemon, Slowpoke, gained an honorable position in that town.