And what did the minions get up to during the hurricane? -- the *actual* story
not_Hydra has just finished frosting the cupcakes when not_SHIELD arrives. With Dr. C in custody, not_Hydra doesn't have tonnes to do besides taking care of the bunnies, and xe has been talking with not_SHIELD a bit more than usual. If xe's honest, the cupcakes are xyr way of getting not_SHIELD to divulge certain work-inappropriate thoughts. Xe hopes that the four dozen xe made will be enough.
not_Hydra is getting suspicious that Dr. C might be defecting to SHIELD, which makes the job transition a point of concern. Xe hasn't been in Hydra's good graces since xe became Dr. C's minion a number of years ago, so xe figures xe has to go with him if he changes sides. The trouble there is the strict fraternisation policy. And, you know, the B&E thing when Dr. C told xem to be careful about the bunnies. (Like xe doesn't know to do that.) And, well, since that one job with the crazy alien guy in the travelling blue box, this is the best gig xe has had for years, and xe really doesn't want to lose this one.
not_SHIELD eats almost all of the cupcakes. not_Hydra isn't really surprised. They wind up in a fort made of not_Hydra's million pillows with the bowl of leftover icing, all set to weather the storm. not_Hydra pushes one of the pillows out the side of the fort so they'll have a window to watch a film or something, if they're so inclined.
They aren't so inclined.
not_Hydra doesn't even steal all of the covers this time. Xe does get up to a bit of no good, but it's partly not_SHIELD's idea, too. They use the rest of the icing from the bowl, put on a spooky film, and pass out in cupcake comas for a few hours, cuddled up together.
In the morning, not_Hydra makes breakfast and convinces not_SHIELD to destroy part of the pillow fort so they can eat it in bed.