The rain and the flu are related. The flu is caused by viruses, but it seems that in Japan a drop of water can totally destroy a person's immune system, making it impossible to prevent the flu and increasing the power of the infection by 1000%; not even the AIDS virus weakens the immune system...
From what I've read in countless manga, the mother will probably come back and be forgiven and the father won't be forgiven. The father will always be painted as the evil one who can't recover, the mothers won't, they're almost always forgiven.
Maruyama is made up of 50% loyalty to his friends and 50% sexual perversion. When he sees the incredible woman next to him, his perversion will be diluted. The new composition will be 40% loyalty to friends, 10% sexual perversity and 50% love.