Saito in the novels version died. He was gone for like a half year. Louise was so tormented by not having him by her that she tried to kill herself so that she could be with him in death. She was stopped and the elf brought Saito back to life, but without his powers. Their re-union, is beautiful.
That is a much better version, much better. Drama, lots of heart wrenching drama.
-Matt
PS. Not to say I didn't enjoy the second season ending, I just wish they had used the original novel ending instead.