The Great Suwa War occured 2300 years ago and was a battle between Suwako Moriya and the gods of Yamato, Kanako Yasaka being one of the gods. The gods of Yamato were victorious.
Suwako Moriya was a ruler of the Kingdom Moriya. She controlled the Mishaguji, who were curse gods that had large amounts of faith, harvests, cursing birth, militaries and many other things. Suwako was the only one who could tame them. However, the gods of Yamato invaded her kingdom. The gods said that they were going to unify all the kingdoms to create a country named Japan. However, Suwako did not wish this to happen and fought back with the most powerful steel weapons around then. She was winning, but one of the gods, Kanako, held out a thin vine that caused Suwako's large steel arsenal to rust instantly. Suwako quickly noticed the difference between her strengths and the gods of Yamato's strengths. Suwako knew she would lose if she continued. She didn't have much of a choice so she surrendered against the gods and relinquished her kingdom.
After that, Kanako Yasaka became the goddess of the Kingdom Moriya. However, the people of Kingdom Moriya could not forget the fear of their native gods, Mishaguji, and were unable to accept their new god. Kanako knew that because of that, she could not gain faith from the people. She gave up on making the kingdom hers. She decided to call forth another god and combined it with Moriya's god. They called this new god, 'Moriya', but was called a different name outside the kingdom. This way, it would seem that 'Moriya' was ruling the kingdom. Thus, Kanako borrowed Suwako's powers and silently rules as God of Mountains.
The new god, 'Moriya' was only a god in name, existing to preserve the legend of Yamato. But the truth was Suwako continued to rule the kingdom. Although the gods of the modern world have been replaced by the Yamato Legends, Suwako still gathers faith.
However, the faith Suwako gathered started fading due to the introduction of the era of science.
Suwako didn't really care, but Kanako panicked and moved the whole shrine to Gensokyo. Suwako didn't know how well she could get by in Gensokyo, but decided to enjoy it as her final amusement. She did not argue with Kanako for deserting the kingdom and going to Gensokyo because Suwako had no regrets left in the outer world.
Kanako's Shrine Maiden and Suwako's descendant, Sanae Kochiya, did not understand why there were 2 gods within her shrine.
Suwako didn't seem to worry if she had been forgotten. She's actually thankful to Kanako for giving her the chance to enjoy a second life in Gensokyo.