From my recollection, after beating Wattson, he will head to his upstairs apartments in New Mauville (This is inaccessible at this point in time). After resolving the Kyogre/Groudon storyline, he can be found in the middle of Mauville in front of the statue. This statue actually is connected to Lumiose in the Kalos region. Watson will explain more when you get that far.
