Yeah this episode stuck with me as well. I seem to recall in the beginning she has a boyfriend and they are both doing this intense physical training to escape like a gauntlet of traps to cross the border. But the boyfriend tells her not to attempt it because she's not good enough or something but she insists to still go. They do the attempt and he escapes and she is caught on the very last trap and injured. She is then put into the factory to build the machinery as punishment while she heals.

Stuff happens, she practices some more and is determined to do the attempt again. The boyfriend becomes a spy with Aeon somehow and they tell her not to do the attempt again but she does it anyway. She makes it all the way and beats the final trap this time only for there to suddenly be a new additional trap added which involves the machinery she built which this time amputates her legs as punishment.

There was also something about a little kid that lived across from her at the beginning that was happy and playing in the beginning and in the final shot the kid is also now a multiple amputee and super sad. It was fucked up.