The boy's father was of course not stupid. He did not spend all those years doing nothing. Being the the malicious overlord's henchmen he was, he risked his immortality, giving it to his master to track down the boy or even indirectly harm him. He knew that the boy was now powerful enough to match up to his powers or even cause him great troubles. He also knew that since the boy had enough positive influence, it was going to be nearly impossible to go along with his original plan. He had to permanently end the boy's life one way or another.
I shuddered at the way the book described it. I remember not really knowing much at all about just how much he wanted me dead when I was that young, even if it was just a few years ago.
Thus he was the one who forced the rain upon the alternate dimension. It rained all night and day, and the water gathered so much as to start flooding the entire city the boy was living in. The city, of course, took action. The girl and the boy barely made it to the city center, in which there were tall skyscrapers. They climbed up to the high levels, and the city prepared its boats so that the citizens could go to a higher, safer location just in case the flood became too bad. The rain continued, on and on, but the city had good technology that managed to keep the flood in check. After forcing the rain for so long, the father was exhausted, and was forced to rest. The father had to find another way to get rid of the potential problem.
NOTE: There were no boats in any dream of mine.