EB: but in the end, you did it to help me, didn't you?
EB: really, i should probably be thanking you!
EB: uh…
EB: are you there?
AG: Yes, I am here.
AG: Sorry, I wasn't sure what to say for a moment.
AG: I am just so incredi8ly relieved you are not angry with me.
This is probably the first time anyone's ever appreciated Vriska’s 'help'.
She's used to (justified) hostility from the trolls. The idea that John would thank her is as alien to her as he is. She can barely comprehend it.
AG: I don't know, John. You'd 8e surprised how often people resent it when you try to help them!
AG: 8ut see, you really get it. That's why you're special.
Well, hang on a second, Vriska.
Tavros resented you for a good fucking reason. Things aren't different because John's 'special', they're different because you're actively treating him better than your last apprentice.
Vriska enjoyed torturing Tavros. Maybe she did think she was ‘helping’ him, but she also knew it was a miserable experience for the guy. There was an undertone of sadism to it that can't be denied, no matter what her true intentions were.
Contrast this with John, who she killed painlessly in his sleep. She didn't torment him, she didn't gloat or insult him, and she went out of her way to make his death as comfortable as possible. Unlike Tavros, Vriska actually cares about John's well-being, and that's why he's more receptive.
John's thankful because he can tell that Vriska cares, and Tavros resented her 'training' because he knew she didn't. Does she really not grok the difference?
AG: I know how this is pro8a8ly going to sound, especially to a human.
AG: 8ut I just killed someone.
And I think you’re having some very unwelcome feelings about it.
Just what is happening to you, Vriska?
AG: He was a friend.
AG: Someone from our team. […]
AG: The truth is I killed him 8ecause at the time, I thought I wanted to, and sort of felt like I finally had to.
I think you killed him because that's what you're trained for. Years of FLARPing with Terezi has trained you to deal with problematic trolls decisively and violently, and years of feeding your lusus has taught you that being a murderer is what defines you. From multiple directions at once, your instincts were screaming that it was time for Tavros to die.
And yet... you're saying you thought you had to kill him. You're not sure anymore - and thus, a small crack begins to form in your worldview.
Vriska Serket is beginning to change.