Ichinensei ni Nacchattara

Takatou Iori, a high school ninensei, was on his way to school to confess his love to classmate Kusanagi Mikuru with a love letter, when he gets ran over by a truck to save a cute elementary schoolgirl.

Summary as of ANN.com:
Main character was a normal high-school 2nd year student, one day while going to school he prevented a accident, but he died saving the little girl. But a passing scientist of justice(Self-proclaimed) saved his life, but due to a lack of part(According to the scientist) he's now a little girl~