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Nightmare Fuel: Runaways
In the "Escape to New York" arc, the Runaways' ally Dagger is attacked (and possibly sexually assaulted) by someone impersonating her partner Cloak. And it turns out that the culprit was a hospital orderly who had access to her room...
During the Civil War tie-in miniseries, SHIELD declares war on the Runaways (because the agency's been taken over by Maria Hill.) In their opening salvo, SHIELD shoots up Victor, tearing his body apart in a horrific manner. As a follow-up, they send a genocidal alternate-universe Kree soldier who snaps Xavin's neck and then captures Xavin and Karolina, as well as Wiccan and Hulkling of the Young Avengers, and sends all four of them to a black site where they're tortured in front of each other by a fat, ugly, mind-rapey creep.
In the "Live Fast" arc, Chase temporarily turns against his teammates in an effort to resurrect Gert. The scary thing is how competent he was at being a villain, easily hobbling Nico and Victor and leaving the rest of the team scrambling to catch up.