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Why it doesn't make sense for Webby to be Scrooge's daughter/clone from plot holes:

Why didn't Bradford use Webby to get the Papyrus as soon as she hatched? In the room where Webby was found, there were toys - if she' was created just for the Papyrus, I doubt they would bother making sure she was having fun - I think they planned to raise that baby as a weapon instead of discarding her afterwards. But that still doesn't explain why Bradford didn't move as fast as he could - this baby babbled and reached for Beakley, she was already at least 4-6 months old in this scene.

Later we find out that Bradford's brothers have been clones all along. If Bradford had the means to create full-grown intelligent clones that do what he says even before he created Webby, why would he wait until Webby was 11 to make May & June? And why did he have to do it with the Stone of What Was + the aging serum if he already had another TWO effective way to make clones? He could've cloned Webby the same way he's cloned himself several times, or just made another Webby from Scrooge's DNA as soon as Beakley stole the original.

On that note, why did he give Scrooge the Missing Mysteries he needed so that Scrooge's family could go get it for him if he was gonna send FOWL after them too? Bradford could've just kept the Missing Mysteries for himself and sent FOWL after them as soon as Beakley stole Webby twelve years ago if he needed the items so bad, that way none of them would've had to fight the McDucks for them.

Bradford was the one to tell Della about the Spear because he knew she'd take it before it was ready. I assume this was his first try to put an end to Scrooge's adventures, which worked wonders and tore the family apart (a perk!), so why did he feel the need to also create Webby for the Papyrus? Again, he didn't even have a way of knowing where the Papyrus was hidden in the first place.

Why Webby could've been Donald/Della's clone instead:

One of the most efficient ways to gather a bird's DNA is from the membrane of the eggs they lay. And who had just laid eggs that were literally due hatching on the same week where Bradford conveniently got rid of her? Della. It would be a lot easier to retrieve some of Della's DNA off the triplets' eggshells from the trashcan than it would be to retrieve a recluse multibillionaire's baby-making DNA (who knows WHAT from).

The Papyrus could only be found by Scrooge's rightful “heir”, not by his direct descendant. Heir is whoever is on Scrooge's will, and that's Donald and Della. Even if Webby was Scrooge's daughter, that wouldn't automatically make her his heir. Cloning Donald/Della would.

Cornelius Coot wasn't just the founder of Duckburg, he was also the person to find a book of "inexhaustible knowledge" from the Lost Library of Alexandria. He gave the book to Clinton Coot (the father of Donald and Della's grandmother), who proceeded to write the JWG from the book's infinite wisdom. Which means not only that Clinton Coot knew Isabella Finch personally, but also that he was the last person who knew where to find the Library of Alexandria. He may have told Isabella Finch about it, and that's how Bradford knew where it was too,

but what if the only people who could access the secret information in the Library had to be Cornelius Coot's descendants? That way, with Quackmore Duck deceased at the time Bradford's plan to get the Papyrus failed in the First Adventure, plus with Donald and Della under Scrooge's impenetrable care, his only way into the Library of Alexandria was to later clone Donald/Della. And that's why he was forced to wait a decade since losing the Papyrus to create Webby, because Della getting pregnant was his best chance.

ALSO THIS IS JUST A REALLY FUN FACT BUT ON THE WEEK THE BOYS HATCHED, IT WAS NEW MOON, AND IF WEBBY WAS MADE FROM THEIR EGGSHELLS IMMEDIATELY AFTER (which explains why she'd be called April also) THEN SHE WAS DUE ON THE 2ND WEEK OF JANUARY THE FOLLOWING YEAR, WHICH WAS ALSO A NEW MOON WEEK. MOON SYMBOLISM ANYBODY??? (If both the triplets and Webby were to be born on new moon, then their birthdates would be April 16-18th 2007 and January 7-8th 2008 respectively btw)

I could probably say more about all of this but it's getting late so I'll keep it at that. I just think this is what the writers were going for before they had to cut off S4 and make-do with scraps.

more about my Three Caballeros Separated AU