>>715226084Smothered with a pillow. People argue that's not possible/realistic, but that's the method.
The body being in the car was suggested somewhere in "the Book of Lost Memories" (special document that details various aspects of the at-the-time trilogy including developer commentary, printed on the reverse side of a japanese SH3 guidebook released in 2003), affirmed in the novelization (adaptation from 2006 that has In Water as its ending and notes the presence of Mary's corpse in the trunk of James' car) and further supported by comments from Masahiro Ito (art director and creature designer, claims the body is in the backseat instead) and, if I remember correctly, Guy Cihi (James' voice actor, claims the body is somewhere else in the car but I don't remember well). The game itself also suggests this with James leaving the room with her body in In Water (this is the suggestion that the BoLM gives, that he's going somewhere with it, not very difficult to figure out). Also all the promotional material of James carrying a body.
This is further "confirmed" (if you're willing to accept it as a source) in the 2024 Remake where Mary's body is literally visible (under some sheets) in the backseat of the car and is very not subtly pointed out in some endings.
Also the Rebirth ending is literally fucking impossible if Mary's body isn't nearby, the town's not doing any damn delivery service unless it's pizza.