It is a fan theory
Nothing concrete supports the theory that Raticate passed away; most that discussion revolves around the fan theory trend called Creepypasta, whose whole premise is tenuously linking together events in video games to make them seem 'creepy' -- as the moniker goes. It's not much to take seriously.
An expanation that fits within the Pokemon canon might be that your rival put Raticate in the PC, but the more likely explanation is that Game Freak simply decided to remove the Pokemon from his team.
More about the 'Poor Rival' fan theory can be found here here. A bit more conversation can be found via Serebii here.
