Headcanon c/p from my tumblr: http://selective-mellowyellow.tumblr.com/post/142909318178/one-of-my-odder-pairings-but-ive-actually-shipped
Zecora actually comes from Celestia and Luna’s era, meeting them sometime after Discord’s defeat. As zebras were shunned and looked down on even worse back then than now, she and Luna bond quickly over their feelings of solitude and she impresses them with her knowledge of magic and potion work and herbalism. She makes home in the Everfree Forest outside of the sisters’ castle, not effected or bothered by it’s strange magic.
In spite of her friendship with Luna, Zecora still gets glances of fear and looks of hate from other ponies, so she easily becomes a night creature and Luna’s almost sole companion. As Luna grows more and more disillusioned with the ‘shunning of her night’ Zecora emphasizes to an extent, understanding ponies not appreciating you. They spend a lot time teaching each other about their kinds of magic and their culture and the creatures that grow and live in the forest and enjoying the night.
But it isn’t enough and one night Luna refuses to allow the sun to rise despite Zecora’s warnings. This lasts for a week before Celestia manages to bring the sun back, in which time the only thing that thrives even in the constant dark is the forest, even when other crops are dying. Luna, changing more and more in her week of dark and shunning everyone, breaks at the sight of the sun and challenges Celestia before transforming into Nightmare Moon and causing her banishment. Zecora, torn between mourning her friend and being overwhelmingly enraged at her for her actions, visits Celestia often as she adjusts to being the now sole ruler and being without her sister. Eventually Zecora is placed in charge of protecting the forest, the old ruins, and the Tree/Elements of Harmony by Celestia, being granted longevity and a greater understanding of alicorn magic. As centuries pass and the forest grows as it will, Zecora loses the location of the Tree, which she deems for the best.
She keeps to herself in the forest, avoiding other ponies and even the moon unless necessary. When her friend returns, it takes Zecora months to warm up to her again until she realizes Nightmare Moon is gone and centuries have passed and Luna is back and she missed her companion terribly and their relationship starts again.
Luna and Zecora eventually marry and adopt an abandoned hippogriff, Aquila. I may or may not have them become Trixie’s mentors in magic, like Celestia [and Zecora once] were for Twilight.