Hou Yi and Chang'E were Originally Mortals
Now things get really complicated. With Hou Yi and Chang'E as mortals, there are multiple versions within versions and depending where you look, you will see both characters being portrayed with varying levels of good and evil.
They all start the same, the 10 Suns appear in the sky, however, this time, instead of being summonded by the Jade Emporer from Heaven, Hou Yi was either summonded from earth, or, he took it upon himself to take down the Suns in an attempt to save humanity.
In some versions Hou Yi urges the Suns to spare humanity before shooting warning shots at them. When both are ignored, he begins shooting them down. In other versions he just starts shooting immediately.
When the Suns are hit in some versions they explode, in some they turn back in to Three-Legged Crows, and in others, they simply die.
In some versions Hou Yi stops shooting at 9 because he wants to leave one Sun to keep the earth warm, in another he only brought 9 arrows, and in another, Di Qun and Xi He beg Hou Yi to show mercy to their last living son.
And once the deed is done, as far as I can tell, all versions agree that it was the Queen Mother of the West that comes to Hou Yi after hearing about his great feat, and bestows upon him an Elixir of Immortality.
Then, there are alternative endings as well. In one version, Hou Yi cannot stand the idea of being separated from his wife, Chang'E, so he asks her to store the elixir for safe keeping. However, one of Hou Yi's students, Pang Meng or Feng Meng (逢蒙 féng méng), wanted the elixir for himself so when Hou Yi was out hunting one day, he tried to take it from Chang'E. Realising Feng Meng's intentions, Chang'E quickly drank the elixir and began to rise to the Heavens. Not wanting to leave Hou Yi, she floated to the Moon - the closest place in Heaven to the earth - so that she could remain close to her beloved husband.
In other versions Chang'E took the elixir through an act of pure selfishness, she took it to maintain her youth, she took it because Hou Yi was unfaithful to her, and there is even a version where Hou Yi claims himself king and becomes a tyrant so Chang'E takes the elixir to ensure his reign would some day come to an end.
As far as I can tell, the version where Chang'E "sacrifices" herself before Feng Meng can take the elixir is the most popular version as this is the official story behind the celebrations for the Mid-Autmn Festival:
After Chang'E floated away, Hou Yi missed her intensely. He would often be found looking up to the moon (where it is said if you look close enough you can still see Chang'E,) with teary eyes. And on each full-moon he would place plates of her favourite foods out on tables for her. As time went on, other locals starting placing offerings on tables and prayed to Chang'E, the Lunar Deity, for good luck and protection.