In his third and fourth battle with you he has a Raticate. Then it leaves his team. You could say he put it in his PC or released it but he was at the Pokemon Tower during his fifth battle.
Why would he be at the Pokemon Tower? Did he want to fight people? He doesn't seem to have caught any Pokemon unless he transfered them into his PC. Even so, he asks you if any of your Pokemon died.
So..His Raticate most likely died. But how does an eleven year old kill a 40 pound rodent monster within a few days? He is a bit cocky and doesn't seem like the safest trainer so he could have overworked it..
Maybe it got poisoned or was seriously injured.