I've seen around an AU where Mary dies and Vermouth takes her place to manipulate Masumi to do the BO's bidding and I raise to you: an AU where Mary shrinks but before she can reach Masumi, Vermouth has already taken her place, only for Masumi to realise about a month in that this is not her mama. Some details include:
When Masumi finds out that this is not Mary (I'm thinking a nighttime phone call to another BO member when Vermouth thought Masumi was asleep), she makes a run for it, reaching out to Shuukichi for help.
Shuukichi tells her to go to the Kudou mansion, that there's an ally there. Shuuichi greets her wearing the Subaru disguise because he's not planning to tell her quite yet. When Shuukichi arrives, there's a hushed disagreement between him and Shuuichi but the disguise stays on for a while. Luckily Masumi isn't paying too much attention because she's very distraught.
Side note: Yukiko and Yūsaku are home too. Yukiko is trying to comfort Masumi without revealing everything.
The big brothers hatch a plan of getting Masumi's stuff away from the hotel she and fake Mary were staying at. Shuukichi pretends to be slightly drunk and overjoyed to see his mother to lure Vermouth out of the room while Masumi and Shuuichi (still in disguise) sneak in and grab Masumi's stuff.
Once the siblings are back at Kudous', Shuukichi all but forces Shuuichi to tell Masumi the truth about him being alive. Masumi, who is still distraught af, breaks down, first trying to fight Shuuichi, then just crying and shouting at him at the same time until he gathers her into an awkward hug so she can cry her heart out in safety.
Meanwhile, Yukiko and Yūsaku are making sure there's a lot of food in the kitchen for when the siblings manage to get up from the library floor.
They also inform Shinichi about this and ask him to help to come up with a lie why Masumi is living at their house. He suggests saying that Masumi and Subaru are very distant cousins and Subaru couldn't let his young cousin move from hotel to hotel when there was plenty of room at the Kudous'.
That first night when Masumi is at the Kudous', Yukiko all but pampers her. She makes Masumi take a bath and washes her hair, talking about how she always wanted a daughter. She makes Masumi some hot chocolate. Forces Shuuichi to let her sleep in the same room with him because she needs family.
Shuuichi realising that he has an annoying soft spot for Masumi and that he's been a jerk to her. He apologises for yelling at her the last time they met and lets her cry against his shoulder until she falls asleep. Holds her through the night because, frankly, he's also shaken about Mary's supposed death and how close he came to losing Masumi as well.
The following week, fake Mary visits Teitan high school a couple of times to look for Masumi. Masumi's absent from school because she's not well. Ran and Sonoko get worried, and Conan has to tell them about Masumi living at the Kudous'. Ran is enraged when she finds out about fake Mary and nearly goes after her the next time she visits Teitan high. Seven of her classmates must hold her back.
About two months after Masumi has moved to the Kudous', the doorbell rings to reveal a preteen girl. Shuuichi opens, dressed as Subaru, and his brain breaks upon seeing a shrunken Mary. They stare at each other for a bit and the only thing he manages to say is "...not dead, then."
When Masumi sees shrunken Mary, she lets out a wail and rushes in to hug her. Mary, not used to being hugged by Masumi, hisses at first, but one stern look from "Subaru" later, she hugs Masumi back.
Mary explains what happened and why it took her so long to find Masumi (she had help from her agency, but needed to take the long route to Japan in order not to alert the BO). Once Mary is done with her explanation, she asks why Masumi is living with this graduate student. This is when Shuuichi takes off the disguise (again), and Mary yells at him for good half an hour.
Once Mary is calm, she, Masumi, and Shuuichi hatch a plan how they can explain to Conan an co. what happened and how to help them bring the BO down.