This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Alien Nine
In episode 4, when Yuri watches the Yellow Knife—wearing the body of Kasumi's older brother—use its duck-billed snout to lift up Kasumi's shirt and enter her abdomen head first. The prone and unconscious Kasumi's response? Giggle and call out to her brother.
Nowhere is there a more textbook warning to the consequences of breaking the cutie than when Yuri snaps after being attacked by a trio of alien-wearing boys...the boys, Yuri and Yuri's teacher are the only things that leave that Alien Storeroom alive. She doesn't stop there though: she returns to the Alien Party room and kills her teammate's empathic alien helmets/partners, who are too paralyzed with her panic attack to resist.
This becomes especially horrific when you view the sequence with the boys' aliens stabbing through Yuri's borg as a metaphor for rape. It gets even worse when you realize that except for her friends, nobody cares that Yuri has been through this experience. Her teacher is more upset about what'll do to her reputation and the dead borgs; her mother just thinks she's overreacting (though in mom's favor, she may not know the whole story); and another teacher Yuri goes to for help tells her to basically "get over it" and do her duty. Yuri does get to spend a nice summer with her friends, but at the end, has to go right back into the same situation that traumatized her in the first place.
Borgs look like amphibian heads with baleen instead of teeth, they have tongues that look like they have mouths of their own (i.e. snake-like) and their diet consists of the sweat off their hosts' backs, which they obtain by licking them. If that wasn't bad enough, the Borg are worn like helmets, their "hands" acting as ear protectors and what holds them in place on the wearer's head. The underside of a Borg—the side that makes contact with the host— is red and nodule-covered...although it is dry, it still looks enough like an orifice to be squick-y. This is even lampshaded: in a poll of schoolgirls, 78% said they didn't want to join an Alien Party because of the attached-to-a-disgusting-alien part.
The end of episode 3: Kasumi shows up at the school grounds with a smile on her face, and Yellow Knife seemingly appears to be friendly, picking her up with amphibian-shaped limbs to toss her in the air into his mouth. Then the screen cuts to black as he audibly gulps her down. Kasumi was still smiling the entire time.
Chapters 18 and 19 of the manga, Yuri Has lost her Borg and has been reduced to an infantile state. Kasumi and Kumi go into a forest filled with aliens to find it. The manga descends into utter horror as Kasumi EVISCERATES monster after monster with her drills and an innocent smile, while Kumi HAS HER ARM TORN OFF to reveal a mass of writhing drills similar to what her borg uses, as she crumples to her knees crying. The worst part? Their teacher planned to send them to the forest at some point, just not so early. It ends with Kumi escaping the forest crawling away on hands and knees from a giant worm in terror, as Kasumi kills it while their teacher looks on. It's heartrending, chilling, and brutal.
It is probably worth remembering that we get hints of the stuff in the above spoiler early on in the series—from the teacher herself. It's not explicitly said, but she was part of an Alien Party herself, when she was their age...and that she got the desirable end state. Oh, and there's actually hints all through the series that this state is to be become a seamless, unified being with your borg... Now reread/rewatch it with this in mind.
Miss Okada's extra story in Emulators, She told a scary story to one of her and Hisakawa's friends, it leaves the lampshade hanging on whether its true or not, but Miss Hisakawa shows up with a bandage over her cheek, which was supposedly the same cheek Okada shot with three tranquilizers.
The Alien Party program? It does exactly what was implied above. The goal is complete and total symbiosis with the borg. The reason all the teachers are so seemingly uncaring when bad things happen to the girls is because as long as they're able to complete the program and fuse, their goals have been met.
And all of this symbiosis is done without actually informing any of the girls what they're getting into, with consequence that two out of three of them lose their humanity before it's too late. Imagine joining an afterschool club, only to find out a couple months in that you're no longer human, and it's much, much too late for you to go back.
And it's not something you get a choice in. When it looks like the program is going to fail because two of the girls are no longer valid candidates, the teacher takes action into her own hands and escalates Yuri's borg to forcibly fuse with Yuri. None of this is done with her consent, and the character in question hates borgs. What's really frightening is that even without fusing with an alien, or using a borg, it's strongly implied that Yuri is turning into one all the same. Slowly.
Kumi's loss of humanity. She doesn't fuse with her borg. She becomes one. And this only becomes apparent chapters after it happens, in the forest chapter mentioned above. Her body at after that point is a paper-thin shell over a mass of drills, one that she explodes out of whenever she needs to fight. Kumi appears wearing gloves and long-sleeves at all times after a certain point because she literally has no arms left- just drills.