What exactly happened at the end of Kamisama no Inai Nichiyoubi? Kamisama no Inai Nichiyoubi (神さまのいない日曜日) ended with more questions than answers:


If Alice died instead of Dee, then why was Dee the one as a ghost in the real world?
Furthermore, Dee has her body (in the outside world) in the final scene.
How does Ai managed to "save" Alice? Yet at the same time she's standing in front of his grave.


Running through the forums and it seems like I'm not the only one who's confused.



What in the world happened? (no pun intended)

The biggest and undeniable contradiction is Dee going from ghost to normal human.
Does this mean that some sort of change of history caused Dee and Alice to "switch places"?
Dee appeared as a ghost because her physical body was still stuck in class 3-4, while Alice had a physical body outside because he was already buried by a proper gravekeeper. Therefore, his body wasn't in class 3-4 like Dee, and could appear normally since he was part of the world outside. 
Dee has a physical body later on, because the world class 3-4 created had been destroyed. Her physical body was released. 
Ai saved Alice by wishing intensely. In Sunday Without God, by wishing for something really badly it somehow would be granted, like how Hampnie Hambart wished to die happily besides his family, or how Alice got the ability Buzzer Beater. When Ai wished for Alice to be saved, God granted that wish, and so Alice could have a physical body outside class 3-4's world and continue to live his life.