Gilgamesh

does the last episode literally kill the entire cast and then everyone on earth and why does the sister come out of w.e that is and stab the other chick etc

The purpose of everyone dying was to start the new line of humans. The copies were angry hard core at not being given a fair chance to fix shit, the originals had their own plan, and nearly succeeded. TeAR, as was said, was the countess pwning the human race, which worked in favor of Gilgamesh's plans. TeAR was to be the new life form that the humans evolved into, starting with her. The sister surviving was not in Gilgamesh's plans, but she happened anyway, due to the little bugger inside her. It protected them. She then fucked over the plans of Gilgamesh royally by killing that little bitch (with that totally freakin' awesome note, 'A'), the broken jealous heart of the countess. From there, a lot of serious incest occurs; or she dies with her child, so that life can start over from there again, the old fashioned way. 'The extremity' was the quote at the end, and I think that means that Kiyoko fucked over everyone involved by dying with the child so that life could hit the reset button. The moral, I believe (with liberal wording), is that you do not fuck with human emotion, and it's power to fuck anyone's plans over.

tl;dr
Holy shit, mind blowing philosophy, the power of love, yadda yadda. Normal humans prevail. We all win (lose).

i still kinda upset with the whole everyone dies, but I understand it had to be like that but, is the sisters tuning fork she's hold supposed to be important, or did they just give her that so she had a weapon to kill the little girl?

The tuning fork is the one she found the day the member from Gilgamesh met them. She kept it with her because it reminded her of a lot of the shit she and Tatsu went through; and as well as to signify the meeting of that dude from Gilgamesh, whom she ended up falling in love with and bearing his seed. Also, she liked pianos hard. But it was something with which to ultimately fuck Gilgamesh over with. She was given that dream once, of wondering who the little girl was; and wondering where she actually was. So after learning all that shit that we learn in the last few episodes, she knows what to do with the fork. Teach that little shit a lesson in fucking with humans. You don't.

edit: Also, in the last minutes of it, it shows Kiyoko leaving with Tatsuya in some ghostly manner, so I think it was actually her child controlling her body. Being her child, it inherited her way of thinking, somewhat, and so had no reservations in doing what needed to be done to give the world a fresh start.