Atrocity's terrifying level includes having to lure the creature into a gas chamber and hit it with knockout gas in order to draw tissue samples from its body. Never knowing if or when Atrocity will wake up from its sedation helps create a pants-crapping atmosphere of tension.
It's quite unsettling to see the CEO's archive room right after The Reveal. It's a shrine dedicated to Peter Parker's past problems and failures, showing just how messed up 2099!Peter Parker really is.
The encounter with Black Cat. She's clearly in the midst of some serious Sanity Slippage, and it's not fully clear if she is ACTUALLY Felicia Hardy or some kind of clone. And all that's been done to her has been at the hands of Peter himself.