It will be something like Chameleon traced Reptile to the incubation chamber (i dont know for what)Right after the energy that emerged from the egg started to possess Reptile Chameleon saves him and the energy possess himself.
Reptile was really hurt and he dissapears somewere scared of what deadly energy he felt possessing him.(So reptile is somewere to leak his wound and reaper for mk 7).
Chameleon used his ability to change his appearance to get the look of Reptile.So everybody thought thath actually Reptile was pessessed but its actually Chameleon.
iN MK 7 he can return to his normal form but with the mind of Onaga or relised from Onagas control and he'll be totally new and original (atleast the story) character.
Its a rough idea but u get it right?