Jay Ross is a junior Detective of the Centerlot Investigation Agency, the head honcho named Tia Celes. Jay is known for being young, inexperienced, and quite stupid. In fact, the opposite of his partner, Carlotta Hume. Bearing the proud name of Special Agent, Carlotta Hume, who Jay affectionately nicknames "Carla", has fourteen years of work under her belt along with the ability to keep a cool head in tough situations. The pair is actually very popular in the agency, their fame (or infamy to some) stemming from Carlotta's sixty-yard dash to catch a criminal to how Jay stopped a gang of thieves by spilling hot chocolate on himself. One day, Tia gives the two an odd assignment: to track down a research team studying the population of nearby Pineville. Recently, the town was inflicted with an odd plague, where each and every individual began to hallucinate that they were... Ponies. Sweet, little ponies. Acting upon the phenomenon, Tia sent in four sociologists and three researchers to record data. That was two months ago, and not a single word from the team. Jay's and Carlotta's job is simple enough, to get in, find the team, and get out. The couple automatically accept this quest.
Upon actually doing the quest, Jay and Carlotta slowly unwrap the true history of the disease and the dark truth about the town. As they dig deeper, they find out that the disease was actually humanly created by a man named Dennis Cord, a former scientist who was fired on suspicions of being a madman. Presumed to be dead until this point, Jay finds out Dennis was only thought to be dead because Tia has an actual hand in the sickness in the town. Jay and Carlotta travel back to the agency and confront Tia about this, who in turns attempts to use bribery, mind games, and finally brute force to persuade them to never talk about the incident. After knocking out half the personnel, Carlotta manages to get the information from Tia at gunpoint. Now fugitives, the duo race back to Pineville, tracking down Dennis and forcing him to revert the chemical process causing the hallucinations, returning the place to normal with only minutes to spare. The police then kick in the door and arrest all three. With an entire town of people as witnesses, Tia, Dennis, and anyone knowing the experiment were put behind bars. Jay and Carlotta receive worldwide attention, and are given medals for their acts of valor against all odds. Ironically, the greenhorn becomes the new head of the agency, his partner - and co-boss - at his side.