Clannad After Story

Once Nagisa dies in child birth, Tomoya pretty much hits rock bottom until Akio and Sanae trick him into spending time alone with his daughter. Where he goes on a trip with her only to end up running into his grandmother who tells him about his "deadbeat" dad and how difficult it was for him when his (Tomoya's father's) wife died. Tomoya realizes he is making the same mistakes that caused him to hate his own father and decides to take care of Ushio himself. During that time Ushio notices light orbs whenever Tomoya manages to have a positive impact in his life or the life of someone else. Once Tomoya and Ushio finally start to become a family she is struck with the same illness that killer Nagisa. She eventually becomes deathly ill and leaves the house during the middle of a cold, winter day. Tomoya finds her, but she dies in his arms, and presumably he dies along with her. Then you find yourself in the Illusionary World where you find that the Garbage Doll is really Tomoya and the young girl is Ushio. A miracle occurs as a result of all of the light orbs, and Tomoya is sent back to the point in time where Nagisa is giving birth, but this time Nagisa surives and they live "happily ever after" as it were. XD

I actually stopped watching the series for a few weeks on the episode when Nagisa died, I thought there was no way they could end the anime correctly in the few episodes they had left, but I'm glad I was pleasantly surprised.