I was worried about that tag and the comments going back and forth, but I took a look at the story and here's how it goes.
Chisa and Ponta are going through some rocky times as Chisa can't have sex due to vaginismus.
She grows fearful that Ponta will start to hate her and wants to find a reason to break up with him first, but can't let go of him no matter what he does. Finally she asks out a coworker who's been trying to seduce her, thinking if she could prove she didn't care so much that she couldn't notice another man's charms she'd feel more sure about dumping him. Instead, she hated herself the whole time and decided to make up instead. Said coworker, Takigawa, convinces her to come to his house to listen to a piano piece he wrote for her and she stupidly follows him thinking since his mother's home she wouldn't be alone. Takigawa proceeds to drug her, send obscene pics to Ponta, then tie her up and torture her after she wakes up until her mind shuts off completely and all she can bring herself to do is wait for it to be over. Afterward, we see for chapter after chapter all kinds of classic signs of rape trauma, leading up to Ponta taking her on a trip in hopes he can help her recover if just a bit.
For those that believe the comments claiming she consented, I'll include a small excerpt I managed to translate:
In order to escape, in order to protect myself, I did exactly as he said. When he undid the ropes like he promised, I'd lost what fight I had left. It doesn't matter anymore. None of it matters one bit. I just want to make this end as quickly as possible. If I close my eyes, it makes no difference who I'm with.
Now tell me, are those really the words of someone who's chosen to have sex with the guy, or those of someone so broken and full of despair that the only thing she can think to do is submit and hope her attacker won't take much longer?
Since netorare does simply mean that one's lover is stolen, a single rape incident could fit. However, given that the text makes it abundantly clear that there was no consent involved, and there are no further events, consensual or otherwise, it's definitely not your standard NTR. And given that, despite the erroneous translation, she found she was completely unable to feel anything for any man besides Ponta, the term is very shaky. That said, the relationship is broken for a while, as Ponta doesn't know how to deal with what happened or accept some of the things she admitted about the incident, while Chisa also can't accept what'd happened, much less accept anyone in her life who sees her as a victim. Even after they get back together the incident continues to loom over them and causes further separations down the road.
A word of advice: don't be too quick to buy whatever disparaging claims people make about this series.