When Chrysalis had chosen to attack Ponyville, she did so as a little bit of an 'espionage mission', and her attack was less of an attack and more of a choreographed scene. She would attack the town during Princess Celestia's visit and during her attack she would search for a suitable subject to use for her nefarious purposes. A new tyrannical dictatorship with love as the central element that simultaneously gives the citizens of her land hope for a better future while keeping them enslaved was hopefully within her grasp.
Then she discovered Fluttershy before the attack, picking flowers and cheerfully telling a nearby friendly squirrel that she was picking them for the arrival of Princess Celestia. Everybody was making a big deal out of the Princess' visit, but Fluttershy had taken the opportunity to offer her freshly picked flowers instead of participating in the festivities or the parade. Chrysalis was suspicious of her true intentions, and she decided to test her suspicions to see if they were accurate.
After watching the entire day being ruined by a swarm of parasprites Chrysalis decided that it was time to make her presence known when the princess appeared on the scene after the conflict had been solved. She used her magical powers and her army of Changelings to terrify the citizens of Ponyville without actually doing any harm. Celestia stood strong in the face of adversity, yet it quickly became obvious that she would take a passive stance during this conflict as she allowed her faithful student and her friends to solve the problem. Chrysalis really couldn't blame her, she knew she wasn't at full power as-of-yet and she suspected that Celestia knew as well. What also became obvious was that when Chrysalis had made herself known Fluttershy immediately ran towards Princess Celestia and hid behind her. When Celestia, noticed the young pony, she moved her wings so that she could shield her from the changeling army and Chrysalis herself whilst glaring at the queen.
It was then that Chrysalis smiled and Celestia's eyes widened with understanding as she realized the changeling queen's intentions. They locked eyes as time seemed to stand still as the battle continued on around them.
"Don't you dare touch her." Celestia's eyes seemed to say as one of her wings attempted to wrap itself relatively tightly around the earth pony who seemed to relax into the touch and momentarily forget about the danger that she had sought sanctuary from. Chrysalis smiled as she took a step towards the sun princess and was amused to hear a slight growl.
"Why not? What does she mean to you?" Chrysalis' eyes asked the princess as she stepped closer towards her.
"She means the same thing to me as I mean to her."
"And what is that exactly?" Chrysalis asked, all the while moving closer towards the princess and the one whom she sought to protect. Celestia seemed to ponder this for a moment as her eyes momentarily seemed to reflect that she was contemplating Chrysalis' silent question. After a few moments of thought, and when Chrysalis had moved close enough to hear her she responded verbally.
"Why does it matter?" Celestia asked, causing Chrysalis to sneer at the princess and turn her gaze towards the earth pony who appeared to be shivering under the warmth of her princess' wing. Her eyes expressing the fear that Chrysalis expected and an emotion that she had spent many years familiarizing herself with. She sneered before her gaze returned to face the princess.
"You and I both now why it matters." Chrysalis claimed as her horn lit up as she began siphoning the small amount love from the princess and the earth pony.
"Two hearts with a capacity for love far greater than most. Who refuse to limit their love to a select few." Chrysalis said as the light emanating from her horn started to increase in brightness as what appeared to be a magical field of energy started to form around them.
"Two hearts with the capacity to find a place in them for everyone in the world. If those two hearts would come together." Chrysalis said as she turned towards the pink-haired earth pony who was now staring at her with a wide-eyed expression.
"If the seed of attraction you two share was planted, if it was allowed to grow into a tree of love. If that love was concentrated and harnessed as a weapon…" Chrysalis paused mid-sentence to witness the look of realization upon Fluttershy's face. "…Then you would not be able to comprehend the amount of power I would have. No one could stand against me and my dream of a new world order would be within my reach."
"But I like our world the way it is now." Flutershy said timidly. "And I like all of the ponies in this world, what would happen to them?" Fluttershy asked, causing Chrysalis to grin wickedly at her two prisoners as the light illuminating her horn disappeared and the filed of magic surrounding them disappeared with it.
"I don't think I'd be the first leader who desires to destroy her kingdom, for the sake of a new world order." Chrysalis said with a smirk as she turned away from her captives who had moved closer to each other during the confrontation.
"The seed has already been planted my dears, whether you realize it or not is of little importance to me." Chrysalis said in an characteristically smug tone as she ordered her changelings retreat, taking time to look behind her and witness the conversation taking place between the element of kindness and the princess of the sun about what had just transpired. The first of many conversations they would have. The changeling observed over the next few years as the relationship between them transformed from attraction, to friendship to love and eventually into marriage. As the two were celebrated throughout the land, Chrysalis decided to make her move. Using her newfound power gained from the imprisonment of the two lovers she was able to take control of the planet she lived on before turning her gaze onto the solar system and then the galaxy itself. Nothing seemed out of her reach. Eventually, the two had a daughter and the child's mother died as she was being born. Fluttershy was heartbroken, yet Chrysalis was petrified. Faced with the possibility of her power source's mortality she made a drastic decision. She travelled into the past with the child in order to warn her past self against her plan's downfall and offer a chance of salvaging her plan with the immortal alicorn child.
Of course, what she didn't expect was for the child to yearn for her mothers. So the twin Chrysalis' from past and future built a life for themselves and their adopted child in the present. Setting the scene in motion to correct the error in their plan as they found love with each other.