My friend and I were playing a video game where a situation occured that led to a brief debate about the application of MLB rules in a certain situation. I figured the intelligent baseball minds here would know the answer to this. The situation is the bases are loaded with one out. A fly ball is hit to left field. A runner at second starts to go to third and is halfway there when the ball is caught. After the ball is caught, meaning two outs, the runner at third tags up. Meanwhile, the runner who was at second remains between second and third for whatever reason. The runner who correctly waited for the ball to be caught and tagged up from third crosses home plate, beating a throw from the left fielder while crossing the plate. The catcher realizes that the runner who started at second never tagged up and is in fact on his way back to avoid getting doubled up. The catcher throws to second before the runner who didn't tag up can return, recording the third out and ending the inning. Our question is does the run scored by the player from third count? Or did the player getting doubled up at second mean the run didn't count? I'd be very appreciate if anyone knew the answer and if there is a specific MLB rule that deals with this.