Cover are a combination of images from here here and with the background from here.
Bon Bon had honestly thought her life as a secret Agent wouldn't come back to haunt her. But, when the Bug Bear returned, she became worried. She meets with Celestia after the wedding, asking if there is anything she should be concerned about.
What Celestia tells her, shocks her to the core. She has a daughter, a clone created from her own DNA from her Agent days on the off-hoof chance she would need replacing. When the agency dissolved, the clone was given to a family, Celestia not knowing Bon Bon hadn't known the clone was still alive or whether or not she'd wanted to keep her as her own daughter.
Now, Bon Bon must find a way to break it to the filly that her life has been a lie. She isn't the pony she thought she was and her family are, tehcnially speaking, not her family.
Motherhood was never said to be easy. Well, when your daughter's a clone of yourself and has lived all her life unaware, it's even harder.
An idea that popped right into my head after a comment Black Gryph0n made during the Bronies React 100th Episode.
In Popular Stories 1-4/8/2015. 
Wow! Thanks, guys! 
Love this idea.
It's great already.
Huh, I'm interested.
Yeeeees...clones! The concept has always intrigued me to the point that I'm using it in my novel, but your take on it has already peaked my attention. Even if we didn't already know each other on the site, I would still so put this on my Read Later list. I am looking forward to seeing the two Sweeties interact and personally hope the maternal factor is really played up, since I'm working on a story about a police officer raising her own clone and doting on her and it is the most gosh darn cute thing ever.
Please pardon my ranting, but this idea is amazing and I am so glad this exists.
This sounds interesting.
I've not read it yet, but it sounds like a interesting story. I do have one potential issue based on the story title and characters tagged.
If this is a story dealing with a clone... from an earth pony.... how does a clone of your own DNA become a unicorn? If magic is your answer... well its not a clone anymore. Clones are identical.
6270983 Well what would you call it then?
Family isn't just about blood. It's about how you have bonds with.
6271383 tube baby?
I'm amazed that no one aside from me noticed the similarities between the two. I originally chalked it up to an design error but this throws things into a new perspective.
6272533 Bonds :3
What a great idea for a story. I've noticed the similarities in their designs and names too.
ALAHU ACKBAR!
THIS IS AWESOME!
Im actually intrested, that's a first in a long time. I want to see where this goes. Like.
Bon Bon: "What about the baker from Starlight Glimmer's town?"
Celestia: "Coincidence."
Bon Bon: "You sure?"
Celestia: "As far as you need to know."
This is a great idea. I'm looking forward to reading even more...
Really, REALLY bodacious concept. I look forward to reading.
"Hey... Lyra? It turns out I've been a mother this whole time! I thought she was dead, but it turns out she just got adopted by Rarity! Neat huh?"
orig02.deviantart.net/f828/f/2011/241/d/8/surprised_lyra_by_pineapplesam-d487v91.png
Wat.
Now it would be the real surprise if it would turn out that Sweetie Belle has some nuckleoid in her DNA from Rarity too like here:
https://derpicdn.net/img/2013/10/25/456345/large.png
...and chapter 2... GO!
...still waiting.
;)
new chapter please
thank you 
This will be an interesting read.
Clone always make things better, Just ask the Galactic Republic.
I have to wonder why no one in the comments made a Metal Gear reference.
When is the next chapter?
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because nobody... I mean nopony cares.
"Don't be mad at me!"
When is the next chapter?
Now this is a nice treat remember this story and quite happy to see it's return. I still find the plot very interesting, so looking forward to seeing where it goes.
I'm just loving all the emotional drama, I certainly feel for poor Bon Bon that's fore sure. Also that little tidbit of Trixie also being a clone of a agent is interesting, and i'm curious to see if it will come up again in the future.
Oh, this will be good.
Ouch this is hitting Bon Bon hard. I hope they find a way to talk about this with her foster parents.
8049545
When is the next chapter?
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9904759
What is the next chapter?
I kinda liked the idea so I'd put it in the tracking folder and then eventually forgot about it.
Obligatory "it's alive"- joke.
See you all in the next chapter in 2023
Looks great
Feels so forced. Why does Bon Bon feel this way? Did she always see the clone as a daughter? Was the HQ attack some traumatic event that left her feeling like part of her was killed? All this drama and no buildup; drama that Sweetie might not care to deal with.
Edit; i know that opinion is unliked but it is valid. There has been no explanation, no buildup just a time skip. No one, but you the author, knows what happened between chapter 1 and 2 to arrive at 2. No idea what they thought to arrive at the conclusions they are working with.
Really interesting story 🙂
Hope you will pick it up again sometime 🙂