The girl doesn't get raped, dude. Averted by the main character who heroically saves the day.
SPOILER The girl in question gets some weird alien juice on her that causes her body to THINK it's going through stages of pregnancy, but thankfully the actual impregnation was stopped. She basically just has to go through the simulated effects of pregnancy like morning sickness, cravings, irritability, engorged breasts, distended belly, etc.
Basically the substance caused her body to prepare itself for the embryo that never got implanted.
P.S. NTR, or Netorare, doesn't mean rape. It means cheating or infidelity. I see SO many people get that wrong.