>>22048763Courtney blamed herself for Team Magma's downfall, and went full yandere trying redeem herself to her boss. Hell, she practically turned herself into a robot just to carry out Maxie's wishes, in the first place. It wasn't until she met you that she started to come out of her shell. And then...well, you saw what happened...
In any case, she's better in the end. You can meet with her after the Delta Episode, where she shows a genuine concern for your wellbeing. Maxie also says you're welcome to visit their hideout, any time.