As Ifurita prepares to enter the Eye of God in order to bring it back under control, and to close the Stable Time Loop which brought about the events of the series:
Ifurita: "This is destiny, Makoto. If I had not undertaken this journey, I could never meet you, and that is why I am going...to meet you - because I had nothing until I met you, not even a single memory."
Makoto "Then let me give you mine." [A Montage of Makoto's memories on Earth with Ifurita placed in them, at peace and happy, follows]
There is the final scene where Ifurita is all alone in the schoolyard, seemingly forever trapped out of her world and time. Suddenly, a slightly older Makoto materializes with her key staff as promised to rescue her and she joyously runs to join him and go home to the tune of a beautiful ballad.
In the manga; Makoto psychically seeing the images of the countless cities that Ifurita destroyed through her eyes; he starts crying at the horror that her existence was. (A much better rendition than the anime, where he was simply confused.)
To make it even better, he just barely smiles. Non-maliciously! And then he tries to carry her off but, since he's a bit of a wimp, he hurts himself. He keeps going anyway. It doesn't make up for anything Jinnai's done, but it is still very sweet.