Chrysalis was scared. She had just lost all of her subjects and no longer had anything. All she had lived for for decades, centuries even, were her subjects. She no longer had any.
 
She ran. All she could do was run. She needed to survive, to breed a new generation of changelings. Not those new, sickeningly vibrant changelings. The real, dark colored, bug-like changelings.
 
After running and running for so long, she comes upon a hidden village, a hidden race of creatures called Kirin.
 
After changing into a pony body she felt comfortable enough in to keep for a while, she stepped into the city and approached the pony she would make fall in love with her.
 
Rain Shine was the leader of the Kirin and a perfect fit to carry Chrysalis’s children. She would fall for Chrysalis and become the mother of the future changelings of Equestria!
 
One problem, though.
 

 
Chrysalis: massaging Rain Shine Is this fine, Rainy?
 
Rain Shine: Of course, my dear.
 
Chrysalis: continues massaging ……..
 
Chrysalis: Rainy, darling, I know we’ve been together for a few months now and…
 
Rain Shine: Yes, dear?
 
Chrysalis: Well, I wanted to know if you’d like to take our relationship to the next level?
 
Rain Shine: gasps, pausing before saying Shutterbug, I’d love to-
 
?: interrupting Rain Shine, the town was wondering when you were signing off on-
 
Chrysalis: interrupting Excuse me, you will address Lady Rain Shine as-
 
 
Chrysalis freezes her movement, shock filling her mind. She met eyes with the most beautiful creature she had seen. She looked like a pony had been set ablaze. She had a fiery red mane and a bright, bubbly look about her. It irked Chrysalis more than it should, but Chrysalis found she couldn’t look away from her, her heart racing. Chrysalis tried to shake the feeling away. It was hatred, it had to be.
 
 
?: Sorry, my name is Autumn Blaze. I haven’t met you yet, but I’m pleased to meet you.
 
Chrysalis: N-Nice to meet you, but as you can tell we are busy at the moment.
 
Rain Shine: Nonsense, dearest. I will go sign some papers, allowing use of the public theater for a religious service and we can go right back to… Rain Shine turns away from Autumn Blaze as she rises, wiggling her eyebrows at Chrysalis our activities and conversation.
 
Autumn Blaze: Thanks Rain Shine!
 
 
Rain Shine disappears from view and Chrysalis is left helpless with Autumn Blaze, not sure what to do or say.
 
 
Autumn Blaze: When Applejack told me that you were roaming not far from our territory, I didn’t believe you would make yourself known, Chrysalis.
 
Chrysalis: shocked What are you talking about?
 
Autumn Blaze: As good of a disguise as that is, I sent your name to them and they checked all Equestria records. There isn’t a record of a “Shutterbug” in any Equestrian databases.
 
Chrysalis: now mad out of fear I swear, you little freak, I will rip your head off your body-
 
Autumn Blaze: laughing Oh no! I won’t tell anybody. I mean, what’s a better chance at turning you good than you living among some of the most temperamental creatures. You gotta be good or you’re gonna set us off.
 
 
Autumn Blaze proceeded to flash her eyes red and wink unashamedly at Chrysalis. Chrysalis’s cheeks flared red and she felt her heart beat faster than it was before, if that were even possible.
 
 
Autumn Blaze: I swear I won’t tell anyone, just… don’t throw away this chance at a new start.
 
 
Autumn Blaze moved closer to Chrysalis, crowding the smaller creature’s space.
 
 
Autumn Blaze: This is a chance for you to find the good in yourself.
 
 
Chrysalis proceeded to look around, seeing no one was in sight and transforming into her true form, the large, dark form towering over Autumn Blaze. Chrysalis flared her nostrils, expecting the small creature to run, but Autumn simply smiled, running her delicate clawed hoof over Chrysalis’s cheek.
 
 
Autumn Blaze: Beautiful
 
 
Chrysalis stood, frozen to her spot, her only movement being transforming back into her pony form as Autumn Blaze walked away.
 
She was left with a strange heat in her chest and a weird feeling in her heart, wondering what spell or magic that tiny pony creature had placed on her.
 
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tl;dr
 
Basically, after the ending I of season 6 of MLP Chrysalis, disguised herself (as the pony you see later in season 9 or so that takes pictures) and ran away from the battle. She found herself in the Kirin village and decided to make a new generation of changelings. She chose the leader of the Kirin to be the mother of her new children. While she was winning the leaders affections, she falls for Autumn Blaze, the spritely and lively creature.