Trixie takes the 1 AM train to Ponyville, disguised in a hat and dress. She pretends to be an Earth Pony, taking care to only use her mouth and hooves instead of her magic. She settles into her room, but she can't sleep because it is too hot.
She nervously moves toward a drinking fountain, using a mirror to check corners and blind spots. Before she can reach the fountain, a turquoise Pegasus gets there first. Trixie has never met her before, but she is Lightning Dust. Lightning Dust gets a drink and walks back to her room, angrily muttering about a "rainbow-maned jerk". Trixie gets her drink while wondering if she was talking about Rainbow Dash. She returns to her room, hopeful that her pursuers will not find her.
Trixie has a nightmare where she's in a white, brightly lit room with Gear Shift, Cover Story, and a female, orange Unicorn with a dark orange mane and purple eyes. Trixie tries to escape, but finds that she's completely paralyzed except for her eyes; she can't even scream. The trio activates a machine with several drills, saws, and other tools that reach for her chest.
Trixie wakes up screaming, only to find it is morning and her chest is unmarked. A member of the train's staff knocks on her door and asks if she is alright, and she says she just had a nightmare.
Lightning Dust stands on the caboose of the train, still angry about the time Rainbow Dash got her kicked out of the Wonderbolts. She turns wistful as she recalls dreams where she did the right thing and remained friends with Dash, then gets surprised that she could ever think positive about Rainbow Dash. Suddenly, she gets confronted by Gear Shift and Cover Story.
Trixie goes to the dining car for breakfast, thankful Ponyville is a few hours away now. She begins to feel paranoid that her pursuers are here and begins scanning the crowd, nearly panicking whenever she spies a pony with similar looks. A waiter asks what she wants and she orders a cheese sandwich and a glass of water. Suddenly, Cover Story enters the car. Trixie desperately tries not to panic and draw attention to herself. Cover Story casts a spell that releases a bright flash of light and everypony except Trixie is now in a trance. He orders everypony to return to their rooms and not come out until and his partner are done with their investigation. Everypony in the car obeys the command as one and file out. Trixie pretends to be one of them, but before she can reach her room, her hat blows off, revealing her horn.
As the two agents chase her, she runs into her room and locks the door. When they break it down, they don't see her and find the window is open. When they look through it, she jumps out of the closet and out the door. She freezes the floor, but the two reveal they are wearing winter horseshoes that allow them to walk on ice. As she runs, she uses everything she can pick up with her telekinesis as a barricade or weapon, but the pair plow through everything. Eventually, she gets on the roof of the train, and has to conjure suction cups so the wind doesn't blow her off. The pair stop chasing her, saying that they had a contingency plan in case she tried that. They decide to sweep the train in case they failed to hypnotize somepony.
As Trixie rests on the roof, she sees Canterlot Mountains up ahead and thinks she just has to hold out a little longer. Suddenly, Lightning Dust appears and attacks her. Trixie defends herself and asks what she wants, but Lightning Dust's eyes and face are devoid of emotion and she stays silent. Her attacker flies up to avoid a tunnel. Trixie ducks, but not quick enough as she feels it clip her hip, drawing blood. As they continue their battle, another train appears, heading in the opposite direction. Suddenly, Rainbow Dash flies over from the other train and knocks Lightning Dust away. As Rainbow takes over the fight, Rainbow says it's a long story why she's out here, while Trixie briefly explains that some strangers are trying to kidnap her. Rainbow notes how strange it is that the normally talkative Lightning Dust is mute. Trixie sees another tunnel ahead and warns them. Rainbow ducks, but Lightning doesn't and her head hits the tunnel.
Horrified, Trixie and Rainbow check on her, only to be shocked to find she's an android. The impact ripped half of her face off, revealing metal, circuitry, leaking oil, and a robotic eye. Rainbow touches the metal and it burns her. Suddenly, Lightning gets up and flashes a light in Rainbow's face before going offline. Recognizing it as the same light that Cover Story used to hypnotize the passengers, Trixie checks on Rainbow, who says she could feel something try to control her, but an aura of blue magic protected her.
Rainbow says they need to get back to the others fast, so Trixie gets on her back and she starts flying towards Ponyville. Rainbow briefly explains how the Tree of Harmony created a map of Equestria they have nicknamed the Cutie Map, which periodically sends members of the Mane Six to deal with problems. Last night, it told her to go to Rainbow Falls. On the train, Spike sent her a letter from Princess Twilight telling her her target was moving towards her, and that was how she found her. Trixie explains everything that has happened to her since last night, lamenting on how she just wants things to go back to normal. Rainbow tries to cheer her up by complimenting her on how she's tough; even after all this excitement, she isn't even breathing hard. Trixie notices Rainbow's Cutie Mark is glowing. Rainbow interprets this as the Cutie Map calling them back, so she tells Trixie to hang on and performs the Sonic Rainboom to speed up their journey.
On the train, Lightning Dust reactivates. She goes back inside and wraps a curtain around her head to disguise her injury, then flies off in pursuit.
In Twilight's castle, Trixie goes to the bathroom to dress her wound and bathe, while Rainbow tells the others what happened. They conclude that the Flim Flam Brothers had already been abducted. Rainbow has Spike send a letter to Gilda warning her about the mysterious strangers, and Gilda replies that so far, there hasn't been any suspicious activity in Griffinstone. Fluttershy sent a letter to Iron Will, but there is no response. She also sent one to Discord, who replied that he's on an interdimensional fishing trip with The Smooze. Twilight briefly suspects Starlight Glimmer is behind this, but decides it doesn't fit her MO. They notice Rainbow has oil with red pigment in it on her, and she says it must have come from Lightning's impact with the tunnel. Then they find a trail of oil leading to the bathroom. Trixie screams. Rainbow quickly breaks the door down, causing Twilight to complain, but the six mares and one dragon stare in shock. Trixie's hip injury has revealed metal, oil, and circuitry. Trixie stares at her injury with as much shock and horror as the others.
