My Little Investigations/Case 1

Boutique break-in
The game opens in Carousel Boutique at 11:08pm; three bipedal, gravelly-voiced creatures ransack the shop in search of something. They find what they're looking for—a large gemstone—when suddenly a nearby window shatters. The three thieves make a hasty retreat while a dazed and confused Scootaloo sits about a pile of broken glass.

The next day, Twilight Sparkle, having heard about the boutique break-in, rushes onto the scene to find Mayor Mare and a hysterical Rarity. They inform Twilight that the True Blue, a large sapphire Rarity had recently come into possession of, and Rarity's cat Opalescence have been stolen. The mayor also informs Twilight that, because of Ponyville's lack of a proper police force, they've hired an investigative team from Canterlot to take on the case, but they won't be arriving to Ponyville for several days. Twilight is mortified to learn that this investigative team is the same one that had bungled a case in Ponyville before. Afraid of what will happen if they get involved, Twilight offers to take on Rarity's case and solve it before they even arrive. Rarity is unsure of the idea, but wishes Twilight good luck all the same. (Throughout the case, Pinkie Pie appears to give Twilight—and the player—gameplay advice.)

Investigation, part 1
Twilight questions Rarity about the night before, to which Rarity says she was stirred from her sleep by a crash downstairs and found that True Blue and Opal were gone. Twilight asks Rarity about anything else she saw, but Rarity is strangely tight-lipped. During her investigation, Twilight finds tire tracks, strands of white hair, and a star-shaped object outside the boutique's broken window. She deduces that the hairs belong to Opal, and whoever made the tire tracks had swerved to avoid her and crashed through the window, making it an accident. She also finds a torn piece of a Cutie Mark Crusaders cape a short distance away from the boutique; asking Rarity about it reveals that it's Apple Bloom's.

As her investigation leads her toward town hall, Twilight finds Apple Bloom speaking with Sweetie Belle. As Sweetie Belle leaves, Twilight talks to Apple Bloom and finds that she's being dodgy and secretive, especially when she brings up Scootaloo. She interrogates the little filly about the night before; when Apple Bloom says she was nowhere near the boutique, Twilight presents the piece of her cape, which was found near the boutique and Rarity testified as belonging to her. Apple Bloom nearly buckles under the pressure, but Twilight beats her to the punch: she's remaining quiet in order to protect Scootaloo. Feeling guilty, Apple Bloom explains that she and her friends were practicing a routine for Rarity's upcoming birthday the night before. During a break, Apple Bloom and Sweetie Belle hung out by the bridge while Scootaloo was nowhere to be found. Around that time, they heard a crash coming from the boutique. A short while after that, they saw Scootaloo racing away from there. Apple Bloom pleads for Twilight to help Scootaloo, who she knows for sure is innocent.

Twilight returns to Rarity and informs her of what she knows: that Apple Bloom had seen Scootaloo crash through her window, and that Scootaloo had stayed at the boutique for a short while before leaving. Rarity is caught in her deceit and apologizes for not being forthcoming earlier. Her testimony is much the same as before—that a crash had woken her up and she rushed downstairs to find True Blue and Opal gone—but she adds that she saw Scootaloo racing out of the boutique. Twilight believes she knows what happened to Opal; she reasons that the tire tracks outside the window were caused by Scootaloo and that the crash was an accident. After a bit of questioning about how Opal was outside to begin with, she also reaches the conclusion that someone else entered the boutique before Scootaloo arrived, allowing Opal to go outside and creating the conditions leading up to the crash. At this pivotal point in her investigation, Twilight decides it's time to talk to Scootaloo herself.

The daring Scootaloo
On her way to the Cutie Mark Crusaders' clubhouse, Twilight runs into Rainbow Dash. She fills Rainbow in on the situation, but when she asks about Scootaloo, Rainbow immediately clams up. With few options open to her, Twilight proceeds to the Crusaders' clubhouse and finds Sweetie Belle standing guard outside. As Twilight chats her up, they hear a commotion from inside the clubhouse, to which Sweetie Belle refuses Twilight entry. In addition, Sweetie Belle mentions that Scootaloo had recently lost something very important to her, causing her even more grief than there would be otherwise. Twilight presents the star-shaped object outside the boutique's broken window, and Sweetie Belle identifies it as half of Scootaloo's lost ribbon, which she'd received from Rainbow Dash and to which Sweetie Belle has the other half. Before returning the restored ribbon to Scootaloo, Twilight chooses to hold onto it for a little longer.

When Twilight returns to Rainbow Dash and shows her the ribbon, Rainbow Dash is caught in her lie. She reveals that she gave the ribbon to Scootaloo a week prior; when she discovered Scootaloo crying out of her inability to fly and her classmates teasing her about it, she gave her the ribbon she'd won in the race that she got her cutie mark during. She also told Scootaloo that if she wanted to get her cutie mark too, she had to "do something really, super daring". Rainbow tells Twilight she didn't say anything in order to preserve her reputation—unfortunately, Apple Bloom was nearby and heard everything. Rainbow leaves, lamenting her ruined image, and Twilight learns from Apple Bloom that Scootaloo is hiding inside the clubhouse. Apple Bloom decides that the only way for Twilight to help Scootaloo is to let them talk, so she makes Twilight an honorary crusader for the day. Together, they return to the clubhouse, and Apple Bloom vouches for Twilight to Sweetie Belle, gaining them entry.

The first confrontation
Scootaloo is naturally upset with Apple Bloom for allowing a "non-Crusader" to enter the clubhouse, but she quickly changes her tune upon learning that Twilight has her ribbon. Using the ribbon as leverage, Twilight confronts Scootaloo about last night.

Scootaloo explains what Twilight already heard from Apple Bloom: that they were practicing a comedy routine for Rarity's birthday. Twilight presses for more info about how long they were practicing, Scootaloo mentions that they were working on the routine nonstop. However, Twilight had learned from Apple Bloom that they took a break, during which time Apple Bloom and Sweetie Belle were by the bridge and Scootaloo was nowhere to be seen, and considering the tire tracks, the ribbon, and Rarity's testimony, Twilight deduces that Scootaloo was in the area of Carousel Boutique. Scootaloo sweats a little but points out that all Twilight has is circumstantial evidence.

When Scootaloo asks Twilight why she would steal from anypony, Twilight reminds her of Rainbow Dash's words—"do something really, super daring" to get her cutie mark—and there are fewer things more daring for a filly to do than commit theft. Scootaloo gets shaken and insists that the only daring thing she was doing was practicing scooter tricks. She was practicing a trick similar to one Rainbow Dash performed at the Best Young Flyer Competition. Twilight naturally comes to the conclusion that, while Scootaloo was practicing her trick, Opalescence leapt out in front of her, causing her to swerve into the boutique window.

Defeated, Scootaloo tells Twilight everything aside from what she already figured out herself. After crashing into the boutique, she saw some dark figures that, startled by the crash, ran away. In the scuffle, she heard one of them trip and growl as well as the sound of something getting ripped. After that, she ran from the scene herself. With this new information, Twilight returns Scootaloo's ribbon and heads back to the boutique.