Tons of trainers for years have wondered about the mystery of Gary’s Raticate that tragically left the game after our battle with Gary on SS Anne.
During this battle we faint the Raticate in question, which we next find Gary in Lavender town’s Pokémon tower filled with Pokémon graves. During this find we battle Gary and notice that his Raticate is missing, alongside the 6th slot of his Pokémon team.
Now this makes things very suspicious as Gary usually makes use of his filled Pokémon spots and doesn’t like to be at a disadvantage. So did we kill Gary’s Raticate on SS Anne? It’s possible as there would be no quick access to a Pokémon Center as we’re in the ocean which risks life for the Pokémon.
As we seen in the anime, battling can take a toll on Pokémon as Pikachu loses to Raichu and is put on a machine to keep it living.
Though the reason we cannot confirm if it died, is because it is not said and Gary also admits when you beat him that he came to the Tower to catch a Cubone and a Marowak. Without any confirmation we can only say that Gary most likely boxed his Raticate in PC storage so he would have space to make use for his new Pokémon to train.
Though he could have an excuse to visit his Raticate at the Pokémon tower as he’s also looking for Cubone and Marowak, with so many possibilities this mystery could go on forever.
This video by The Game Theorists below also has some good ideas about the mystery: