So, if y'all are familiar with the fan-game, My Little Investigations, listen up (for those who aren't, you may want to check it out first). I was watching a playthrough of that game (I can't play it, unfortunately), and it triggered something in my brain that made me want to create something like that. So I came up with a case that I think would be perfect for this game.
So here's the case: Fluttershy has a small swampy habitat that is used to shelter certain creatures that cannot handle sunlight. To ensure of this, the swamp is surrounded by thick vegitation, including various exotic flowers. Among those flowers are a type called "Giant Butterfly Blossoms", which are very large, beautiful flowers, which Fluttershy was also growing for the annual butterfly migration. Ten of these flowers are pink, but when Fluttershy went to check on some of the tadpoles that live in the swamp, she found that four of those flowers were missing, chopped right off of their vines. She concludes that these flowers were stolen, and judging from the condition of the vines, the theft happened five days ago!
Before the official investigation can begin, however, the infamous Canterlot Investgative Team (who are being analyzed by Princess Celestia due to the complaints that she's been getting) already have their prime suspect: Sweetie Belle. Their conclusion is that Sweetie Belle stole the four flowers to poison Apple Bloom (who's been sick for the past three days) with them. However, the only evidence that they have is that the missing flowers were found in the Cutie Mark Crusaders' clubhouse, and Fluttershy's tip that these flowers have toxins in them that make them unfit for consumption, which is hardly even circumstantial. So while the duo are continuing their investigation, Twilight takes the case and does some investigating on her own.
Although the this game shares the same features as the one made by Equestrian Dreamers, there are a couple key differences. First off, when you partner up with Fluttershy, you will be able to communicate with animals, which comes in handy since the crime happened in a remote swamp that (spoiler alert) only Fluttershy knows about. Second, while the origional game had a traditional two-way confrontation, which involves one character trying to make a point and the other trying to establish their innocence, this one includes a four-way confrontation, in which the investigators have to defend their opponents' suspect and the suspects are trying to establish their innocence own at the same time.
So who stole Fluttershy's Giant Pink Butterfly Blossoms? Since I plan on giving updates on this, only time will tell. And as the story developes, the answer may surprise you!