When we’re actually the bad guys.
The most compelling point of this is that we transfer the Pokemon, not release, transfer, to Professor Willow, like he’s collecting them for something
Ironically, it used to be releasing Pokemon, but in the beta that got a lot of complaints because people would catch Pokemon, use them in gym battles, and then, instead of healing them, release them, discarding them now that they were done with them. People thought that treating Pokemon like they were disposable felt too evil, like something Team Rocket would do, so Niantic changed it to transferring the Pokemon to Willow.